Difference between revisions of "Lenaolufson Week 10"

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[[User:Lenaolufson | Lena Olufson]]
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== Overview ==
 
== Overview ==
  
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#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.
 
#* You will also use these articles to write the Introduction and Discussion sections of your Final Project Report.
  
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=== Grading for this assignment ===
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== Annotated Bibliography of Genomics Papers for your Species ==
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* Your individual journal entry for this week is worth a total of 15 points (instead of 10).
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* 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.
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== Individual Journal Assignment ==
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* 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).
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* Link from your user page to this Assignment page.
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* Link to your journal entry from your user page.
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* Link back from your journal entry to your user page.
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* Don't forget to add the "Journal Entry" category to the end of your wiki page.
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**'''''Note: you can easily fulfill all of these links by adding them to your template and then using your template on your journal entry.'''''
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* 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.
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'''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.'''
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=== Annotated Bibliography of Genomics Papers for your Species ===
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For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.
 
For this assignment, you will be creating an annotated bibliography of genomics papers for your team's species.
  
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* On your individual journal entry pages, you will keep an electronic lab notebook that details how you conducted your search, along with the results of your search.
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===Journal Article for Whole Genome Sequencing===
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* On your team page (see shared assignment below), you will combine your results with your teammates into one final, ranked bibliography.  Specifically, you need to search the literature/biological databases for the following:
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*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.  
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*# The journal article which describes the results of the whole genome sequencing for your species. ''(Note that you will be giving a journal club presentation on this article for your [[Week 11]] assignment.)''
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*Use a keyword search for each of these databases/tools and answer the following:   
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*#* Use a keyword search for each of these databases/tools and answer the following:   
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** '''PubMed'''
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*#** '''PubMed'''
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***What original keyword(s) did you use?  How many results did you get?
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*#*** What original keyword(s) did you use?  How many results did you get?
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****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.
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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****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.
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*#** '''Google Scholar'''
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*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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*#*** What original keyword(s) did you use?  How many results did you get?
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**** 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.
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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**'''Google Scholar'''
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*#** '''Web of Science'''
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***What original keyword(s) did you use?  How many results did you get?
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*#*** What original keyword(s) did you use?  How many results did you get?
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****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.
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*#*** Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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***Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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*#* Use the advanced search functions for each of these three databases/tools and answer the following:   
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****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.
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*#** '''PubMed'''
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**'''Web of Science'''
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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***What original keyword(s) did you use?  How many results did you get?
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*#** '''Google Scholar'''
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****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.
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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***Which terms in which combinations were most useful to narrow down the search?  How many results did you get after narrowing the search?
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*#** '''Web of Science'''
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****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.
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*Use the advanced search functions for each of these three databases/tools and answer the following:   
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*#* Each of the references in your bibliography needs to have the following information (an example is given in another section below):
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**'''PubMed'''
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*#** 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).)
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***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#** The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
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****I went to the advanced PubMed search immediately as directed by Dr. D in class, see answer above for PubMed.
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*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ PubMedCentral].
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**'''Google Scholar'''
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*#** The link to the full text of the article (HTML format) from the publisher web site.
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***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#** The link to the full PDF version of the article from the publisher web site.
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****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.
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*#** Who owns the rights to the article?
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**'''Web of Science'''
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*#*** Does the journal own the copyright?
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***Which advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#*** Do the authors own the copyright?
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****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.
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*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
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*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.
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*#*** Is the article available “Open Access”?
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*The link to the abstract: http://www.ncbi.nlm.nih.gov/pubmed/26067980
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*#** 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 [http://www.plos.org/ Public Library of Science] or [http://www.plos.org/ BioMedCentral], or predatory open access organization, see the list of) [http://oaspa.org/membership/members/ (Open Access Scholarly Publishers Association Members) here.]
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*The link to the full text of the article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4463544/
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*#** Is this article available in print or online only?
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*The link to the full text of the article (HTML format): http://genomea.asm.org/content/3/3/e00657-15.long
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*#** Has LMU paid a subscription or other fee for your access to this article?
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*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
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*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
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*Who owns the rights to the article?
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*#* Give an overview of the results of the search.
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**Does the journal own the copyright?
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*#** How many articles does this article cite?
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***No.
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*#** How many articles cite this article?
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**Do the authors own the copyright?
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*#** 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?
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***Yes.
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*# 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.
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**Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
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*#* 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.
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***Yes.
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*#* 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.
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**Is the article available “Open Access”?
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*#* State what you used as search terms and what type of search terms they were.
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***Yes.
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*#* Give an overview of the results of the search.
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**What organization is the publisher of the article?  What type of organization is it?   
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*#** How many results did you get?
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***Published by the American Society for Microbiology online.  
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*#** Give an assessment of how relevant the results were.
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**Is this article available in print or online only?
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*#* For each article, please provide all of the same information that you provided for the genome article above.
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***Online only.
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*#* In addition, you must also link to the web site where the microarray data resides.
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**Has LMU paid a subscription or other fee for your access to this article?
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*#** For each of the microarray articles/datasets, answer the following:
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***Yes.
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*#**# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
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* Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
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*#**# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
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**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.
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*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
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*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
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*#**** Click on the link to "Browse ArrayExpress"
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*#**** Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
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*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
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*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
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*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
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*#*** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
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*#* On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through eight in order of preference for using the dataset for your project.  The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.
+
  
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==== Sample Bibliographic Entry ====
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===Journal Article Bibliographic Entry 1===  
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*I used the ArrayExpress database to find the data concerning Bordetella pertussis.  
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For example, see the bibliographic entry for Schade et al. (2004) below which is available both in print and online:
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* State what you used as search terms and what type of search terms they were.
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+
**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".
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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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* Give an overview of the results of the search.
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* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
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** How many results did you get?
 +
***There were 13 experiments provided.  
 +
** Give an assessment of how relevant the results were.
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***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, while the others compared data collected from other strains of bacteria as well.
 +
*Brickman, T. J., Cummings, C. A., Liew, S.-Y., Relman, D. A., & Armstrong, S. K. (2011). Transcriptional Profiling of the Iron Starvation Response in Bordetella pertussis Provides New Insights into Siderophore Utilization and Virulence Gene Expression . Journal of Bacteriology, 193(18), 4798–4812. http://doi.org/10.1128/JB.05136-11
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* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
 
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
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* Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
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*PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/?term=Transcriptional+Profiling+of+the+Iron+Starvation+Response+in+Bordetella+pertussis+Provides+New+Insights+into+Siderophore+Utilization+and+Virulence+Gene+Expression
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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 (HTML): http://jb.asm.org/content/193/18/4798.full
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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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* Publisher Full Text (PDF):  http://jb.asm.org/content/193/18/4798.full.pdf+html  
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* Publisher:  American Society for Cell Biology (scientific society)
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* Copyright:  2011 by the American Society for Microbiology
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* Publisher:  Journal of Bacteriology
 
* Availability:  in print and online
 
* Availability:  in print and online
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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: yes
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*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3263/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
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== Team Journal Assignment ==
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*What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
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**The experiment that was performed in this study examined the changes of the full genome sequence of B. pertussis in response to iron starvation conducted in vitro. The treatment of the experiment was normalized bacterial suspension prepared form iron-repleted and iron-depleted SS cultures. These cultures were incubated with rabbit RBC and then analyzed throughout the experiment. The controls of the experiment were hemoglobin released in the absence of bacteria and by hypotonic lysis of rabbit RBC using water.
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=== Team Membership ===
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*Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
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**According to the array express abstract links there were 56 results for the Samples and Data, however there were only two different source names that appeared but there were many entries for both.
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The project groups are:
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# '''Heavy Metal HaterZ''' (a.k.a. Team 1) - ''Shewanella oneidensis''
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#* Coder: Mary Alverson
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#* Quality Assurance: Josh Kuroda
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#* GenMAPP Users: Ron Legaspi & Emily Simso
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# Team 2: ''Bordetella pertussis''
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#* Coder: Nicole Anguiano
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#* Quality Assurance: Brandon Klein
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#* GenMAPP Users: Lena Olufson & Mahrad Saeedi
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# '''GÉNialOMICS''' - ''Burkholderia cenocepacia''
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#* Coder: Anu Varshneya (Project Manager)
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#* Quality Assurance: Brandon Litvak
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#* GenMAPP Users: Veronica Pacheco & Kevin Wyllie
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# Team 4 - ''Shigella flexneri''
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#* Coder: Jake Woodlee
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#* Quality Assurance: Trixie Roque
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#* GenMAPP Users: Erich Yanoschik & Kristen Zebrowski
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* Choose one member of your team to be the Project Manager. Only ''one'' member of the team will serve in this role (no co-Project Managers).  Record this information on the [[Gene_Database_Project | Group Project page]] and on your team's home page.
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=== Selecting Your Team's Species ===
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Each team will choose from among the species shown below:
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* ''Burkholderia cenocepacia''
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* ''Bordetella pertussis''
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* ''Shewanella oneidensis''
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* ''Shigella flexneri''
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=== Creating a Team Wiki Page ===
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From this week on, your "Shared Journal Assignments" will become "Team Journal Assignments".  For this week, some preliminary tasks are assigned to your team to kickstart your final projects.
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* Name your team and create your team home page on the wiki. 
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** The name of your team home page should simply be the team name.
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** This page will be the main place from which your team project will be managed. Include all of the information/links that you think will be useful for your team to communicate with each other and with the instructors. Hint:  the kinds of things that are on your own User pages and on the course Main page can be used as a guide.
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** Create a link to your team's page on the course Main page.
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** Create a category using your team name and use it on your team's main page and all pages you will create for the project.  Also use the category "Group Projects" on your team's pages.
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** Create a template for your team with useful information and links that you will use on all pages that you will create for the project.
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* On your team wiki page, compile a single annotated bibliography for your group (including the bibliographic citations, links, and answers to questions about the papers) with the genome paper from your species and the microarray papers ranked one through eight in order of preference for using the dataset for your project. The instructors will review your results to make sure that the data are suitable for the project before you move forward with the analysis.
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===Journal Article Bibliographic Entry 2===
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*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, while the others compared data collected from other strains of bacteria as well.
 +
*Cummings, C. A., Bootsma, H. J., Relman, D. A., & Miller, J. F. (2006). Species-and strain-specific control of a complex, flexible regulon by Bordetella BvgAS. Journal of bacteriology, 188(5), 1775-1785.
 +
* ArrayExpress Abstract: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 +
* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426559/
 +
*PubMed Abstract:http://www.ncbi.nlm.nih.gov/pubmed/?term=Species-+and+Strain-Specific+Control+of+a+Complex%2C+Flexible+Regulon+by+Bordetella+BvgAS
 +
* Publisher Full Text (HTML): http://jb.asm.org/content/188/5/1775.full
 +
* Publisher Full Text (PDF):  http://jb.asm.org/content/188/5/1775.full.pdf+html
 +
* Copyright:  2006 by the American Society for Microbiology
 +
* Publisher:  Journal of Bacteriology
 +
* Availability:  in print and online
 +
* Did LMU pay a fee for this article: yes
 +
*Link to where the microarray data resides: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-29/?keywords=&organism=Bordetella+pertussis&exptype%5B%5D=%22rna+assay%22&exptype%5B%5D=%22array+assay%22&array=
 +
*What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
 +
**This study compared strains and species of Bordetella and studied their spectrum of gene expression states. The experiment consisted of a series of steps of labeling, nucleic acid extraction, labeling, bioassay data transformation, growing, specifying biomaterial action, and combining into a pool. There were wild types used in this experiment on the various strains.
 +
*Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
 +
**When I went to the Samples and Data page from the ArrayExpress abstract page, there were 56 results that appeared in the table. There were five different strain names and four different organisms used, with some wild types included as well.
  
 +
{{Lenaolufson}}
 
[[Category:Assignment]]
 
[[Category:Assignment]]
 
[[Category:Group Projects]]
 
[[Category:Group Projects]]

Latest revision as of 07:15, 10 November 2015

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


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