Difference between revisions of "Lenaolufson Week 10"

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***What original keyword(s) did you use?  How many results did you get?
 
***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.  
 
****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  
+
****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?
 
*** 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'''
 
**'''Google Scholar'''
 
***What original keyword(s) did you use?  How many results did you get?
 
***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?
 
***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'''
 
**'''Web of Science'''
 
***What original keyword(s) did you use?  How many results did you get?
 
***What original keyword(s) did you use?  How many results did you get?
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**'''PubMed'''
 
**'''PubMed'''
 
***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
***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'''
 
**'''Google Scholar'''
 
***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
**'''Web of Science'''
 
**'''Web of Science'''
 
***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 
***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
 +
 
*Each of the references in your bibliography needs to have the following information (an example is given in another section below):
 
*Each of the references in your bibliography needs to have the following information (an example is given in another section below):
 
**The complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide])  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 complete bibliographic reference in the APA style (see the [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide])  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).)

Revision as of 06:54, 9 November 2015

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.

Grading for this assignment

  • Your individual journal entry for this week is worth a total of 15 points (instead of 10).
  • Your team journal entry for this week is worth a total of 10 points (instead of 3). Each member of the team will receive the same grade for the team journal entry.

Individual Journal Assignment

  • Store this journal entry as "username Week 10" (i.e., this is the text to place between the square brackets when you link to this page).
  • Link from your user page to this Assignment page.
  • Link to your journal entry from your user page.
  • Link back from your journal entry to your user page.
  • Don't forget to add the "Journal Entry" category to the end of your wiki page.
    • Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.
  • For your assignment this week, you will keep an electronic laboratory notebook on your individual journal entry page for this week. An electronic laboratory notebook records all the manipulations you perform on the data and the answers to the questions throughout the protocol. Like a paper lab notebook found in a wet lab, it should contain enough information so that you or someone else could reproduce what you did using only the information from the notebook.

Note that each person will complete an individual annotated bibliography. Information from each team member's bibliography will then be compiled on your team's page. This will require coordination among the team members so that both the individual and team assignment will be completed by the journal deadline.

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?
      • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the 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?
        • 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?
    • Web of Science
      • Which advanced search functions were most useful to narrow down the search? How many results did you get?
  • Each of the references in your bibliography needs to have the following information (an example is given in another section below):
    • The complete bibliographic reference in the APA style (see the Writing LibGuide) 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?
      • Does the journal own the copyright?
      • Do the authors own the copyright?
      • Do the authors own the rights under a Creative Commons license?
      • Is the article available “Open Access”?
    2. Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database.
      • Give an overview of the results of the search.
        • How many articles does this article cite?
        • How many articles cite this article?
        • Based on the titles and abstracts of the papers, what type of research directions have been taken now that the genome for that organism has been sequenced?
    3. Each person needs to find 1-2 potential journal articles that refer to public/published microarray data for your species than are different than what your teammates have found. Thus, each team should find 4-8 articles. If you cannot find a minimum of four articles, please let the instructors know right away.
      • The experiments must be measuring gene expression aka transcriptional profiling or transcription profiling by array. Microarrays can also be used for other types of experiments, but these won't be suitable for analysis.
      • We recommend that you begin by searching for the data, and then by finding the journal article related to the data. State which database you used to find the data and article.
        • I used the ArrayExpress database to find the data concerning Bordetella pertussis.
      • State what you used as search terms and what type of search terms they were.
        • I used the filters in order to narrow down my search; I filtered by organism Bordetella pertussis, experiment type "rna assay", and experiment type "array assay".
      • Give an overview of the results of the search.
        • How many results did you get?
          • There were 13 experiments provided.
        • Give an assessment of how relevant the results were.
          • All of the results were relevant enough to be considered as a possible candidate for a microarray paper that can be used for this assignment at first glance. However, after looking through the results more, there were only 3 results that focused on Bordetella pertussis bacteria by themselves.
      • For each article, please provide all of the same information that you provided for the genome article above.

Journal Article Bibliographic Entry 1

Sample Bibliographic Entry

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

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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