Lenaolufson Week 10

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Lena Olufson

Overview

The two main objectives of this week's exercise is to:

  1. Create your team's home page, select your species, and select your Project Manager.
  2. Create an annotated bibliography of papers from which you will derive data for your final research project. This is the second Assignment in the course that specifically addresses the requirements to fulfill the Information Literacy flag for the course.
    • Two members of your team will present one of the primary research articles (genome or microarray paper) as a journal club presentation on Tuesday, November 17; the other two members of your team will present the other primary research article as a journal club presentation on Tuesday, November 24.
    • You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.

Annotated Bibliography of Genomics Papers for your Species

For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.

Journal Article for Whole Genome Sequencing

  • Note: I was not the member of my group who discovered the genome sequencing paper that we ultimately are using for our species, but I did conduct my own searches as described below.
  • Use a keyword search for each of these databases/tools and answer the following:
    • PubMed
      • What original keyword(s) did you use? How many results did you get?
        • It is important to always go directly to the advanced search when searching on PubMed so that the search can be refined immediately since there are so many available articles through this cite.
        • I started off using the search keywords of bordetella pertussis and limiting the search with the Title/Abstract filter. This came back with 4,778 results which was not ideal.
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • To further narrow down my search I used the keywords genome sequence under the Text Word category and proceeded to see my results again. This time I received 17 results, and they were all much more relevant to my desired article.
    • Google Scholar
      • What original keyword(s) did you use? How many results did you get?
        • I started off using the keywords in the search bar as bordetella pertussis genome and received 22,500 results in 0.07 sec. This was way to many and I had to continue to narrow down my search.
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
        • I next added the keyword sequence to the end of my previous search, so the whole search now read bordetella pertussis genome sequence. However, this gave me still 20,500 results which is far too many. I next tried adjusting the date range of the articles and I selected the Since 2015 time frame. This gave me 934 results, which was a great improvement to the thousands I generated before. After reading the titles of many of the most relevant articles, a lot of the results are very useful, although it would take some time to try and find a very good one since there are so many to choose from by using this search engine.
    • Web of Science
      • What original keyword(s) did you use? How many results did you get?
        • I started off using the search keywords bordetella pertussis and received 5,768 results. This is too many and I need to refine my search to narrow down the 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 refined my search keywords by adding genome sequence to the end of my previous search so it read bordetella pertussis genome sequence, and this search generated 139 results. By using the filter for sorting by, I was able to sort the results from the highest number of times cited to the lowest, and this really helped me to find the most relevant and popular articles.
  • 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?
        • I went to the advanced PubMed search immediately as directed by Dr. D in class, see answer above for PubMed.
    • Google Scholar
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • Using the advanced search, I searched for articles with all of the words bordetella pertussis genome sequence anywhere in the article, as well as the date range from 2014-2015. This still gave me quite a large number of results which was 2,200. I tried refining my results by using the article published by j biol chem, but this only gave me back 2 results. Google scholar was difficult to use for me because it had such large numbers of articles when I conduced my searches and it was hard to narrow down the article with filters. I would have liked to figure out if there was a way for me to filter the articles from most amount of times cited to least because this would have helped me find the most relevant and popular articles.
    • Web of Science
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
        • I was very successful with a search I tried from the beginning, and that was to search for the keywords bordetella pertussis genome sequence whole. This gave me back only 21 results, and I was able to filter them from number of citations in order to seek out the most relevant articles.
  • Boinett, C. J., Harris, S. R., Langridge, G. C., Trainor, E. A., Merkel, T. J., & Parkhill, J. (2015). Complete genome sequence of Bordetella pertussis D420. Genome announcements, 3(3), e00657-15.
  • The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
  • The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
  • The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
  • The link to the full PDF version of the article from the publisher web site: http://genomea.asm.org/content/3/3/e00657-15.full.pdf+html
  • Who owns the rights to the article?
    • Does the journal own the copyright?
      • No.
    • Do the authors own the copyright?
      • Yes.
    • Do the authors own the rights under a Creative Commons license?
      • Yes.
    • Is the article available “Open Access”?
      • Yes.
    • What organization is the publisher of the article? What type of organization is it?
      • Published by the American Society for Microbiology online.
    • Is this article available in print or online only?
      • Online only.
    • Has LMU paid a subscription or other fee for your access to this article?
      • Yes.
  • Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
    • I was unable to find my specific article in the web of science database, and I tried multiple times searching different keywords and the authors, but my genome sequence article was nowhere to be found. I was unsure of how to proceed and so I was not able to conduct a prospective search.

Journal Article Bibliographic Entry 1

Journal Article Bibliographic Entry 2

Loyola Marymount University: website


Weekly Assignments Individual Journal Pages Shared Journal Pages
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