Jwoodlee Week 10

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Annotated Bibliography of Genomics Papers for your Species

      • Use a keyword search for each of these databases/tools and answer the following:
      • I searched the name of the search tool on google and then clicked on the first link in order to access each of these. For example, I googled "pub med", clicked on the first result, and then entered the following keywords into the search bar on PubMed.
        • PubMed
          • What original keyword(s) did you use? How many results did you get?
            • I searched on PubMed: "full genome shigella flexneri" and got 20 results. I searched "genome shigella flexneri" and got 664 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 got pretty narrow search results from this search, 20 results is very manageable. However, with that said, the results I got were not very helpful. I changed my search by eliminating the "full" in the beginning and got 664 results and while this is way more to sift through the results were much more useful and I got some candidates for our full genome sequence paper.
        • Google Scholar
          • What original keyword(s) did you use? How many results did you get?
            • I searched "shigella flexneri full genome" and got 24,500 results. This isn't really surprising considering that Google Scholar searches the entire web whereas PubMed only searches their database.
          • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
            • I narrowed my search on Google scholar by typing "shigella flexneri full genome complete" this narrowed down the results to 18,400 hits instead of the original 24,500. I feel like I could narrow it down much more drastically if I used the advanced search option.
        • Web of Science
          • What original keyword(s) did you use? How many results did you get?
            • I searched "Shigella Flexneri genome" and got 590 results.
          • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
            • "Shigella Flexneri genome complete" narrowed down the search to 147 results, however I feel a lot of results still aren't relevant, with advanced searching I feel like I could be more effective.
      • 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 used search by Title/Abstract and used "Shigella Flexneri genome" as my search term. I got 5 results and they all seemed pretty promising. Much more effective than the keyword general search.
        • Google Scholar
          • Which advanced search functions were most useful to narrow down the search? How many results did you get?
            • "shigella flexneri genome" went into the "all of the words" field, and I made it so the words had to occur in the title of the article. Also, the article had to be published between 1997 and 2010, I chose these dates because I figured that was a realistic range. I got 8 results in return that were all very good. The article we ultimately chose was the very first result actually.
        • Web of Science
          • Which advanced search functions were most useful to narrow down the search? How many results did you get?
            • I found that searching by title wasn't all that helpful for whatever reason. For my advanced search I filtered by topic: "shigella flexneri genome" and by title "shigella flexneri" because I figured if it didn't have shigella flexneri in the title it wasn't worth looking for. Also I filtered the year from 1997-2010 again because that seems like a realistic date.

Overall I would say PubMed or Google Scholar especially are good resources if looking for an article off the bat, they have more effective options for advanced searching. With that said, I think Web of Science is still a useful in tool in other ways once an article has already been found.

Microarray paper:

The complete bibliographic reference in the APA style:

  • Fu H, Liu L, Zhang X, Zhu Y, Zhao L, Peng J, et al. (2012) Common Changes in Global Gene Expression Induced by RNA Polymerase Inhibitors in shigella flexneri. PLoS ONE 7(3): e33240. doi:10.1371/journal.pone.0033240

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?

  • Copyright: © 2012 Fu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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? (commercial, for-profit publisher, scientific society, respected open access organization like Public Library of Science or BioMedCentral, or predatory open access organization, see the list of) (Open Access Scholarly Publishers Association Members) here.

  • Plos One is the publisher/Journal. It hosts open access research articles. (Public Library of Science)

Is this article available in print or online only?

  • Online only from what I can see.

Has LMU paid a subscription or other fee for your access to this article?

  • No LMU has not paid a subscription or other fee because it is open access on the Public Library of Science.

Use the genome sequencing article you found to perform a prospective search in the ISI Web of Science/Knowledge database. How many articles does this article cite?

  • 25 cited references

How many articles cite this article?

  • 0 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?

  • Well given that there are no papers that cite this paper there hasn't been anything done to build on this specific topic. In regards to the genome I think this paper has built on the work of the people who sequenced the first genome of Shigella flexneri as well as the other micro array papers.

State which database you used to find the data and article.

  • ArrayExpress

State what you used as search terms and what type of search terms they were.

  • "shigella flexneri" filtered by organism, experiment type:"rna assay", experiment type: "array assay"

Give an overview of the results of the search.

  • 7 results returned with 6 viable options due to the number assays.

How many results did you get?

  • 7

Give an assessment of how relevant the results were.

  • Very relevant, 6/7 results were viable.

In addition, you must also link to the web site where the microarray data resides.

For each of the microarray articles/datasets, answer the following: What experiment was performed? What was the "treatment" and what was the "control" in the experiment?

  • Drugs(RNA Polymerase Inhibitors) were added to Shigella flexneri in order to see if bacteria became less active. The control was a group of bacteria with no drugs added to them, and the treatment was a group of bacteria with drugs added to them.

Were replicate experiments of the "treatment" and "control" conditions conducted? Were these biological or technical replicates? How many of each?

  • There are two drugs RX and RP with 6 samples per drug. The experiment was run 3 times which yielded 36 assays. I believe that means 3 biological replicates and 12 technical replicates within each experiment, but I am not 100 percent sure.


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