Difference between revisions of "Hhinsch Week 11"

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==Bibliography Notes==
 
==Bibliography Notes==
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*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).)
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** The link to the abstract from PubMed.
 
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** The link to the full text of the article in PubMedCentral.
 
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** The link to the full text of the article (HTML format) from the publisher web site.
 
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** The link to the full PDF version of the article from the publisher web site.
 
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** Who owns the rights to the article and what is the availability?
 
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*** Does the journal or the authors own the copyright?
 
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*** Is the article available “Open Access” upon publication under a Creative Commons license?
 
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*** 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? 
 
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*** 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)
 
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** Is this article available in print or online only?
 
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*** Has LMU paid a subscription or other fee for your access to this article?
 
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** 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:
 
* 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:   
 
* Use a keyword search for the first three databases/tools and answer the following:   
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*** 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
 
*** 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?
 
**** How many articles does this article cite?
 +
*****This article cites 144 references.
 
**** How many articles cite this article?
 
**** 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
 
*** 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?
 
**** How many articles does this article cite?
 +
*****This article cites 108 references.
 
**** How many articles cite this article?
 
**** 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
 
*** 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?
 
**** How many articles does this article cite?
 +
*****This article cites 76 references.
 
**** How many articles cite this article?
 
**** How many articles cite this article?
 +
*****258 articles cite this article.
  
 
==Bibliography==
 
==Bibliography==
−
For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:
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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
 
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
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* Publisher Full Text (HTML):  https://link.springer.com/article/10.1007/s11538-015-0092-6
 
* 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
 
* Publisher Full Text (PDF):  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/pdf/11538_2015_Article_92.pdf
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* 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.
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* Copyright: The Author(s) 2015. Open Access: 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.
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* Publisher: Bulletin of Mathematical Biology
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* Publisher: Bulletin of Mathematical Biology(scientific society)
 
* Availability: Online
 
* Availability: Online
 
* Did LMU pay a fee for this article: No
 
* Did LMU pay a fee for this article: No
 +
* Data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4636536/bin/11538_2015_92_MOESM1_ESM.zip
  
  
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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
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Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x
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* PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/15483057
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* PubMed Abstract:  https://www.ncbi.nlm.nih.gov/pubmed/16989656
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* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
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* PubMed Central:  N/A
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* Publisher Full Text (HTML):  http://www.molbiolcell.org/content/15/12/5492.long
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* Publisher Full Text (HTML):  https://academic.oup.com/femsyr/article/7/2/244/616825?searchresult=1
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* Publisher Full Text (PDF):  http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
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* Publisher Full Text (PDF):  http://onlinelibrary.wiley.com/doi/10.1111/j.1567-1364.2006.00162.x/epdf
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* 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
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* Copyright:  Copyright © 2007, Oxford University Press; Open Access after time has elapsed: 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. You must ask permission from the publisher to use the article.
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* Publisher:  American Society for Cell Biology (scientific society)
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* Publisher:  Published by Oxford University Press(respected open access organization)
−
* Availability:  in print and online
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* Availability:  Online and in print
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* Did LMU pay a fee for this article: no
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* Did LMU pay a fee for this article: No
 +
* Data: I couldn't find any supplementary data other than the data provided in the article.
  
 
==Acknowledgments==
 
==Acknowledgments==
 +
#Dr. Dahlquist helped the QA's and Data Analysts learn what to look for and how to navigate Web of Science.
 +
#I worked with [[User:Mbalducc|Mary Balducci]] over text and in class in order to complete the deliverables of this assignment.
 +
#I worked with my team members,[[User:Mbalducc|Mary Balducci]], [[user:ArashLari| Arash Lari]] and [[user:nicolekalcic| Nicole Kalcic]] on the creation of our [[Page Desiigner| team page]].
 +
#While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.[[User:Hhinsch|Hhinsch]] ([[User talk:Hhinsch|talk]]) 22:28, 13 November 2017 (PST)
 +
 
==References==
 
==References==
−
 
+
#Web of Science. (2017). Retrieved November 13, 2017, from https://login.webofknowledge.com/error/Error?Error=IPError&PathInfo=%2F&RouterURL=https%3A%2F%2Fwww.webofknowledge.com%2F&Domain=.webofknowledge.com&Src=IP&Alias=WOK5
−
{{PageDesiigner}}
+
#LMU BioDB 2017. (2017). Week 11. Retrieved November 13, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
 +
#PubMed. (2017). Retrieved November 13, 2017 from https://www.ncbi.nlm.nih.gov/pubmed
 +
#Google Scholar. (2017). Retrieved November 13, 2017 from https://scholar.google.com/
 +
#Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x
 +
#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
 +
{{Pagedesiigner}}
 
{{hhinsch}}
 
{{hhinsch}}

Latest revision as of 06:34, 14 November 2017

Bibliography Notes

  • 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

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


Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x

Acknowledgments

  1. Dr. Dahlquist helped the QA's and Data Analysts learn what to look for and how to navigate Web of Science.
  2. I worked with Mary Balducci over text and in class in order to complete the deliverables of this assignment.
  3. I worked with my team members,Mary Balducci, Arash Lari and Nicole Kalcic on the creation of our team page.
  4. While I worked with the people noted above, this individual journal entry was completed by me and not copied from another source.Hhinsch (talk) 22:28, 13 November 2017 (PST)

References

  1. Web of Science. (2017). Retrieved November 13, 2017, from https://login.webofknowledge.com/error/Error?Error=IPError&PathInfo=%2F&RouterURL=https%3A%2F%2Fwww.webofknowledge.com%2F&Domain=.webofknowledge.com&Src=IP&Alias=WOK5
  2. LMU BioDB 2017. (2017). Week 11. Retrieved November 13, 2017, from https://xmlpipedb.cs.lmu.edu/biodb/fall2017/index.php/Week_11
  3. PubMed. (2017). Retrieved November 13, 2017 from https://www.ncbi.nlm.nih.gov/pubmed
  4. Google Scholar. (2017). Retrieved November 13, 2017 from https://scholar.google.com/
  5. Ando, A., Nakamura, T., Murata, Y., Takagi, H. and Shima, J. (2007), Identification and classification of genes required for tolerance to freeze–thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Research, 7: 244–253. doi:10.1111/j.1567-1364.2006.00162.x
  6. 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
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