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=== Annotated Bibliography of Genomics Papers for your Species ===
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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.
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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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* 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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#** '''PubMed'''
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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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#*** What original keyword(s) did you use?  How many results did you get?
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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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#**** First, I searched "pertussis", and got 29,674 results. Realizing that was too broad, I searched for "bordetella pertussis", and got 11,829 results. After, I searched "bordetella pertussis genome", and got 757 results, then I searched "bordetella pertussis genome sequence", and got 530 results.  
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*#* Use a keyword search for each of these databases/tools and answer the following:   
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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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*#** '''PubMed'''
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#**** Searching "bordetella pertussis genome sequence" was the most useful combination to narrow the search. It reduced the number of results from 29,674 to 530. An advanced search would likely decrease the number of results further.
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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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*#**** First, I searched "pertussis", and got 29,674 results. Realizing that was too broad, I searched for "bordetella pertussis", and got 11,829 results. After, I searched "bordetella pertussis genome", and got 757 results, then I searched "bordetella pertussis genome sequence", and got 530 results.  
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#*** What original keyword(s) did you use?  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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#**** I began by using the same combinations of keywords as I used for Pubmed to see how Google Scholar would compare. A search for "pertussis" resulted in 336,000 results, which was noticeably more than Pubmed. Searching "bordetella pertussis" resulted in 54,900 results. "bordetella pertussis genome" resulted in 22,500 results, and "bordetella pertussis genome sequence" resulted in 20,500 results. It was apparent that there were far too many results to be useful with the search results that I'd used before on Pubmed. However, I knew that it an advanced search would be necessary in order to narrow down the results further.
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*#**** Searching "bordetella pertussis genome sequence" was the most useful combination to narrow the search. It reduced the number of results from 29,674 to 530. An advanced search would likely decrease the number of results further.
+
#*** 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'''
+
#**** Similarly to Pubmed, the search for "bordetella pertussis genome sequence" resulted in the fewest results. However, it was still 22,500 results, which was far too many to work with. This was much more manageabel than the 336,000 results initially returned by the "pertussis" search, but still far too many. An advanced search would be necessary.
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*#*** What original keyword(s) did you use?  How many results did you get?
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#** '''Web of Science'''
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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?
+
#*** What original keyword(s) did you use?  How many results did you get?
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*#** '''Web of Science'''
+
#**** I used the same keywords that I'd used above for both Pubmed and Google Scholar. The search for "pertussis" returned 111,582 results, a value much larger than the number of results returned from Pubmed, but much less than Google Scholar. A search for "bordetella pertussis" returned 34,582 results. "bordetella pertussis genome" returned 415 results, and "bordetella pertussis genome sequence" returned 285 results.
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*#*** 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?
−
*#*** 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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#**** The search for "bordetella pertussis genome sequence" returned 285 results, significantly less than both Pubmed and Google Scholar.
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*#* Use the advanced search functions for each of these three databases/tools and answer the following:   
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#* Use the advanced search functions for each of these three databases/tools and answer the following:   
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*#** '''PubMed'''
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#** '''PubMed'''
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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 advanced search functions were most useful to narrow down the search?  How many results did you get?
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*#** '''Google Scholar'''
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#**** The very first search I conducted was "Title/Abstract" containing "bordetella pertussis genome", which returned 7 results. A search for "bordetella pertussis genome sequence" in the title or abstract returned 19 results. The fact that the latter search returned more results was surprising to me, but it seemed that the results were more related to what I was looking for in comparison to the results returned by the former.
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*#*** Which advanced search functions were most useful to narrow down the search?  How many results did you get?
+
#** '''Google Scholar'''
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*#** '''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?
+
#**** The first search I conducted was "bordetella pertussis genome", where all the words were contained in the title. There were 40 results. I then searched "bordetella pertussis genome sequence" with the same filters, predicting that it would result in more results than the previous search. However, I was incorrect. This search resulted in only 10 results.
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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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#** '''Web of Science'''
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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 first searched "bordetella pertussis genome" with the "title" filter on. This resulted in 38 results. A search for "bordetella pertussis genome sequence" with the same filter gave 26 results.
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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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#* After searching, I selected a paper from Pubmed that contained information about the ''Bordetella pertussis'' genome.
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*#** The link to the full text of the article (HTML format) from the publisher web site.
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#** Andrade, B., Marin, M., Cambuy, D., Fonseca, E., Souza, N., & Vicente, A. (2014). Complete genome sequence of a clinical Bordetella pertussis isolate from Brazil. Memórias Do Instituto Oswaldo Cruz, 109(7), 952-954. doi:10.1590/0074-0276140288
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*#** The link to the full PDF version of the article from the publisher web site.
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#*** PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25411007
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*#** Who owns the rights to the article?
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#*** PubMed Central:  http://www.ncbi.nlm.nih.gov/pubmed/25411007
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*#*** Does the journal own the copyright?
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#*** Publisher Full Text (HTML):  http://memorias.ioc.fiocruz.br/issues/past-issues/item/2271-0288_complete-genome-sequence-of-a-clinical-bordetella-pertussis-isolate-from-brazil
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*#*** Do the authors own the copyright?
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#*** Publisher Full Text (PDF):  http://memorias.ioc.fiocruz.br/issues/past-issues/item/download/2993_09efb65acbb113b4dab6e5190f1ac99c
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*#*** Do the authors own the rights under a [http://creativecommons.org/ Creative Commons] license?
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#*** Copyright:  2014 by Instituto Oswaldo Cruz - Fundação Oswaldo Cruz - Ministério da Saúde (information found on website); open access
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*#*** Is the article available “Open Access”?
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#*** Publisher: Oswaldo Cruz Foundation (scientific society)
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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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#*** Availability:  in print and online
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*#** Is this article available in print or online only?
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#*** Did LMU pay a fee for this article: no
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*#** Has LMU paid a subscription or other fee for your access to this article?
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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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*# Use the genome sequencing article you found to perform a ''prospective'' search in the ISI Web of Science/Knowledge database.
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#* Give an overview of the results of the search.
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*#* Give an overview of the results of the search.
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#** How many articles does this article cite?
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*#** How many articles does this article cite?
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#*** 13
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*#** How many articles cite this article?
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#** How many articles cite this article?
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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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#*** 1
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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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#** 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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*#* 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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#*** It's difficult to say, since only one article cited the paper. The paper seems to be a review article discussing pertussis strains and pediatrics. From this, I can assume that the main direction has been discussing how to treat whooping cough.
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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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# 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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*#* State what you used as search terms and what type of search terms they were.
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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.
−
*#* Give an overview of the results of the search.
+
#* 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.
−
*#** How many results did you get?
+
#* State what you used as search terms and what type of search terms they were.
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*#** Give an assessment of how relevant the results were.
+
#* Give an overview of the results of the search.
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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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#** On array express, I searched by organism "Bordetella pertussis", "RNA Assay", and "Array Assay".
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*#* In addition, you must also link to the web site where the microarray data resides.
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#** How many results did you get?
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*#** For each of the microarray articles/datasets, answer the following:
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#*** 13.
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*#**# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
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#** Give an assessment of how relevant the results were.
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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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#*** Only the top 3 results were for purely Bordetella pertussis. The rest were varying combinations of pertussis and other strains of Bordetella.
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*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
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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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*#*** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] ('''''recommended''''')
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#* In addition, you must also link to the web site where the microarray data resides.
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*#**** Click on the link to "Browse ArrayExpress"
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#* Bibliography 1: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/
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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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#** Brinig, M., Register, K., Ackermann, M., & Relman, D. (2006). Genomic features of Bordetella parapertussis clades with distinct host species specificity. Genome Biology, 7(9). doi:doi:10.1186/gb-2006-7-9-r81
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*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
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#*** PubMed Abstract:  http://www.ncbi.nlm.nih.gov/pubmed/16956413?dopt=Abstract&holding=f1000,f1000m,isrctn
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*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
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#*** PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1794550/
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*#*** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)]
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#*** Publisher Full Text (HTML):  http://www.genomebiology.com/2006/7/9/R81
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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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#*** Publisher Full Text (PDF):  http://www.genomebiology.com/content/pdf/gb-2006-7-9-r81.pdf
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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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#*** Copyright: Brinig et al.; licensee BioMed Central Ltd. (information found on the article); open access
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#*** Publisher: BioMed Central Ltd (for-profit publisher)
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==== Sample Bibliographic Entry ====
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#*** Availability:  online
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#*** Did LMU pay a fee for this article: no
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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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#**# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
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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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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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#* Bibliography 2: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
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* PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
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#** Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006
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* PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
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#*** PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/16484188?dopt=Abstract
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* Publisher Full Text (HTML):  http://www.molbiolcell.org/content/15/12/5492.long
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#*** PubMed Central:  http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1426559/
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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/188/5/1775.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/188/5/1775.full.pdf
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* Publisher:  American Society for Cell Biology (scientific society)
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#*** Copyright: American Society for Microbiology; open access
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* Availability:  in print and online
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#*** Publisher:  American Society for Microbiology (professional organization for scientists)
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* Did LMU pay a fee for this article: no
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#*** Availability:  online and in print
 +
#*** Did LMU pay a fee for this article: no
 +
#**# What experiment was performed?  What was the "treatment" and what was the "control" in the experiment?
 +
#**# Were replicate experiments of the "treatment" and "control" conditions conducted?  Were these biological or technical replicates?  How many of each?
  
 
== Links ==
 
== Links ==
 
{{Template:Nanguiano}}
 
{{Template:Nanguiano}}

Latest revision as of 03:28, 10 November 2015

Annotated Bibliography of Genomics Papers for your Species

  1. 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.)
    • 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?
          • First, I searched "pertussis", and got 29,674 results. Realizing that was too broad, I searched for "bordetella pertussis", and got 11,829 results. After, I searched "bordetella pertussis genome", and got 757 results, then I searched "bordetella pertussis genome sequence", and got 530 results.
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
          • Searching "bordetella pertussis genome sequence" was the most useful combination to narrow the search. It reduced the number of results from 29,674 to 530. An advanced search would likely decrease the number of results further.
      • Google Scholar
        • What original keyword(s) did you use? How many results did you get?
          • I began by using the same combinations of keywords as I used for Pubmed to see how Google Scholar would compare. A search for "pertussis" resulted in 336,000 results, which was noticeably more than Pubmed. Searching "bordetella pertussis" resulted in 54,900 results. "bordetella pertussis genome" resulted in 22,500 results, and "bordetella pertussis genome sequence" resulted in 20,500 results. It was apparent that there were far too many results to be useful with the search results that I'd used before on Pubmed. However, I knew that it an advanced search would be necessary in order to narrow down the results further.
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
          • Similarly to Pubmed, the search for "bordetella pertussis genome sequence" resulted in the fewest results. However, it was still 22,500 results, which was far too many to work with. This was much more manageabel than the 336,000 results initially returned by the "pertussis" search, but still far too many. An advanced search would be necessary.
      • Web of Science
        • What original keyword(s) did you use? How many results did you get?
          • I used the same keywords that I'd used above for both Pubmed and Google Scholar. The search for "pertussis" returned 111,582 results, a value much larger than the number of results returned from Pubmed, but much less than Google Scholar. A search for "bordetella pertussis" returned 34,582 results. "bordetella pertussis genome" returned 415 results, and "bordetella pertussis genome sequence" returned 285 results.
        • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
          • The search for "bordetella pertussis genome sequence" returned 285 results, significantly less than both Pubmed and Google Scholar.
    • 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?
          • The very first search I conducted was "Title/Abstract" containing "bordetella pertussis genome", which returned 7 results. A search for "bordetella pertussis genome sequence" in the title or abstract returned 19 results. The fact that the latter search returned more results was surprising to me, but it seemed that the results were more related to what I was looking for in comparison to the results returned by the former.
      • Google Scholar
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          • The first search I conducted was "bordetella pertussis genome", where all the words were contained in the title. There were 40 results. I then searched "bordetella pertussis genome sequence" with the same filters, predicting that it would result in more results than the previous search. However, I was incorrect. This search resulted in only 10 results.
      • Web of Science
        • Which advanced search functions were most useful to narrow down the search? How many results did you get?
          • I first searched "bordetella pertussis genome" with the "title" filter on. This resulted in 38 results. A search for "bordetella pertussis genome sequence" with the same filter gave 26 results.
    • After searching, I selected a paper from Pubmed that contained information about the Bordetella pertussis genome.
  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?
        • 13
      • How many articles cite this article?
        • 1
      • 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?
        • It's difficult to say, since only one article cited the paper. The paper seems to be a review article discussing pertussis strains and pediatrics. From this, I can assume that the main direction has been discussing how to treat whooping cough.
  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.
    • State what you used as search terms and what type of search terms they were.
    • Give an overview of the results of the search.
      • On array express, I searched by organism "Bordetella pertussis", "RNA Assay", and "Array Assay".
      • How many results did you get?
        • 13.
      • Give an assessment of how relevant the results were.
        • Only the top 3 results were for purely Bordetella pertussis. The rest were varying combinations of pertussis and other strains of Bordetella.
    • For each article, please provide all of the same information that you provided for the genome article above.
    • In addition, you must also link to the web site where the microarray data resides.
    • Bibliography 1: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-95/
    • Bibliography 2: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-28/
      • Cummings, C., Bootsma, H., Relman, D., & Miller, J. (2006). Species- and Strain-Specific Control of a Complex, Flexible Regulon by Bordetella BvgAS. Journal of Bacteriology, 188(5), 1775-1785. doi:doi: 10.1128/JB.188.5.1775-1785.2006
        1. What experiment was performed? What was the "treatment" and what was the "control" in the experiment?
        2. Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

Links

Nicole Anguiano
BIOL 367, Fall 2015

Assignment Links
Individual Journals
Shared Journals
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