Difference between revisions of "Bklein7 Week 10"

Revision as of 01:34, 6 November 2015

Instructions

Class Instructions

• Find...
  1. Genome Sequence Paper.
     • Select canonical bacteria strain / paper
     • Should only have a handful to compare
  2. Microarray data/paper
     • This is where the data comes from
     • Each individual chooses 2
     • All 8 will be ranked in the final submission
• Individual Journal
  • Electronic Notebook
    • details your individual research process
    • answers questions
    • personal annotated bibliography
• Team Journal
  • Post team annotated bibliography (order 8 microarray papers)

Assignment Page: 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.

• 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.
• 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:
  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?
         • Which terms in which combinations were most useful to narrow down the search? How many results did you get after narrowing the search?
       • Google Scholar
         • 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?
       • 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?
       • 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”?
       • 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.
       • Is this article available in print or online only?
       • Has LMU paid a subscription or other fee for your access to this article?
  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.
     • State what you used as search terms and what type of search terms they were.
     • Give an overview of the results of the search.
       • How many results did you get?
       • Give an assessment of how relevant the results were.
     • 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.
       • For each of the microarray articles/datasets, answer the following:
         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?
       • Remember, microarray data is not centrally located on the web. Some major sources are:
         • EBI ArrayExpress (recommended)
           • Click on the link to "Browse ArrayExpress"
           • Use the drop down "Filter Search Results" to filter datasets by your organism, by "RNA assay" and "Array assay" to narrow your search.
         • NCBI GEO
         • Stanford Microarray Database
         • PUMAdb (Princeton Microarray Database)
         • In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
     • 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.

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

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/15483057
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC532028/
• Publisher Full Text (HTML): http://www.molbiolcell.org/content/15/12/5492.long
• Publisher Full Text (PDF): http://www.molbiolcell.org/content/15/12/5492.full.pdf+html
• 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
• Publisher: American Society for Cell Biology (scientific society)
• Availability: in print and online
• Did LMU pay a fee for this article: no

Researching Bordetella pertussis Genomics Papers in the Public Domain

Important Links:

• LMU Biology LibGuide
• BIOL/CMSI BioDB LibGuide

Searching the Literature for a Genome Sequence Paper for Bordetella pertussis

Conducting Keyword Searches Using PubMed, Google Scholar, and the Web of Science.

• PubMed
  • Original Keyword Search: Bordetella pertussis genome
    • Results: 757
  • Narrowing the Search
    • Added the keyword sequence
      • Search: Bordetella pertussis genome sequence; Results: 530
      • This addition was moderately helpful in narrowing the search results.
    • Added the keyword complete and sequence
      • Search: Bordetella pertussis complete genome sequence; Results: 36
      • This addition was very helpful in significantly narrowing the search results (much more so than the addition of just the keyword sequence).
      • The list of papers retrieved using this search was easy to manually review.
      • 5 Bordetella pertussis genome sequence papers were retrieved in the list of 36 results.
• Google Scholar
  • Original Keyword Search: Bordetella pertussis genome
    • Results: 22,500
    • The number of results retrieved by Google Scholar was significantly larger than the number of results retrieved by PubMed for the same search, indicating the wider scope of Google Scholar searches.
  • Narrowing the Search
    • Added the keyword sequence
      • Search: Bordetella pertussis genome sequence; Results: 20,500
      • This adjustment to the search was not very helpful.
    • Added the keyword complete and sequence
      • Search: Bordetella pertussis complete genome sequence; Results: 17,700 results
      • This adjust to the search was also only somewhat helpful in narrowing down the results (like in PubMed, this keyword was a more helpful addition than sequence).
      • Most of the top search results included genome sequences for bacteria other then Bordetella pertussis, indicating the need for advanced search functions and filters to sort through this data.
        • Although Google Scholar casts a wide net, this is sometimes not useful, as it brings up junk results.
• Web of Science
  • Original Keyword Search: Bordetella pertussis genome
    • Results: 415
    • Evidently, the Web of Science appears to be the smallest of the three databases in which I have been searching.
  • Narrowing the Search
    • Added the keyword sequence
      • Search: Bordetella pertussis genome sequence; Results: 285
      • This adjustment to the search was helpful in narrowing the search.
    • Added the keyword complete and sequence
      • Search: Bordetella pertussis complete genome sequence; Results: 50
      • As in the other databases, the keyword complete was a more helpful keyword in narrowing results than sequence.
      • The results from this search were able to be manually reviewed.
      • 7 Bordetella pertussis genome sequence papers were retrieved out of the 50 retrieved results.
        • Note: These 7 papers all occurred at the very end of the results list and were therefore were not the easiest to find. I think it would be more intuitive for these results to have been presented first, although there are filters I could play with to make this happen. It is just surprising to me that the default filter doesn't appear to be one based on relevance.

Conducting Advanced Searches Using PubMed, Google Scholar, and the Web of Science.

• PubMed
  • I began with the original keyword search conducted on PubMed: Bordetella pertussis genome (Results: 757)
    • Originally, changing keywords narrowed the search down to 36 results.
  • This search was successfully narrowed down further than it had been during any keyword searches using advanced searches.
    • Searching for "Bordetella pertussis genome" only in the Title/Abstract of papers significantly narrowed down the search results
      • Search: Bordetella pertussis genome[Title/Abstract]
      • Results: 7
      • 2 Bordetella pertussis genome sequence papers were retrieved out of the 7 results.
        • I was surprised to find that, although a better ratio of relevant papers was retrieved, not all of the genome papers found in the original keyword searches were retrieved in this fashion.
  • By searching for the best keyword result of "Bordetella pertussis complete genome sequence" using the Title/Abstract advanced search, the most efficient search was conducted.
    • Search: Bordetella pertussis complete genome sequence[Title/Abstract]
    • Results: 9
      • Surprisingly, this more precise advanced search yielded more results, suggesting that keyword order is important to the advanced search algorithm.
      • 4 Bordetella pertussis genome sequence papers were retrieved out of the 9 results.
• Google Scholar
  • Building off of the success of [Title/Abstract] searches in PubMed, I decided to try the Google Scholar advanced search where all keywords must occur in the title of retrieved articles.
    • Search 1: "allintitle: Bordetella pertussis genome"
      • Results: 40
      • This advanced search successfully narrowed down the Google Scholar search results for this keyword search from 22,500 to 40, a number that is easy to manually assess!
      • 8 Bordetella pertussis genome sequence papers were retrieved out of the 40 results.
    • Search 2: "allintitle: Bordetella pertussis complete genome"
    • Results: 5
      • I chose to add the most useful of the two keyword additions I had been using, complete, to the allintitle advanced search. This resulted in the most narrow search witnessed thus far in my investigation of the literature (5 results). This is particularly interesting because this narrow search occurred in the largest database.
      • 5 Bordetella pertussis genome sequence papers were retrieved out of the 5 results.
      • This 100% accuracy was tied for the best witnessed out of any advanced search.
• Web of Science
  • As with PubMed and Google Scholar, I found title advanced searches to be the most useful in narrowing my results.
    • Search 1: "TITLE: (Bordetella pertussis genome)"
      • Results: 38
      • This search was better than the most narrow keyword search produced, which yielded 50 search results. However, I felt as though adding additional keywords to the title advanced search would be more effective than manually sorting through 38 records.
    • Search 2: "TITLE: (Bordetella pertussis complete genome)"
      • Results: 5
      • As in Google Scholar, adding the more successful keyword complete significantly narrowed down the search results to just 5 records!
      • 5 Bordetella pertussis genome sequence papers were retrieved out of the 5 results.
      • This 100% accuracy was tied for the best witnessed out of any advanced search.
      • It is impressive that this same result was yielded by the smallest database in addition to the largest database.
    • Note: I found the option to filter papers by the number of times they were cited in the Web of Science to be useful.

Genome Sequencing Article Citation:

Complete Genome Sequence of Bordetella pertussis CS, a Chinese Pertussis Vaccine Strain

Genome Sequencing Article Prospective Search:

• This article cites 16 sources.
• Since its publication in 2011, this article has been cited by 7 sources.
• By assessing the titles of the 7 papers that cited this article using the Web of Science, I was able to determine the type of research directions that have been taken using the genome sequence for Bordetella pertussis:
  1. Assessment of proteins secreted by Bordetella pertussis such as Pertussis Toxin, and how genetic mutations effect the functions of these proteins.
  2. Evolution of virulence in pathogenic bacteria.
  3. Creating better vaccines.

Finding Microarray Papers involving Bordetella pertussis.

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.

• How many results did you get?
• Give an assessment of how relevant the results were.

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.

• For each of the microarray articles/datasets, answer the following:
  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?

Annotated Bibliography

Microarray Papers:

King, A. J., van der Lee, S., Mohangoo, A., van Gent, M., van der Ark, A., & van de Waterbeemd, B. (2013). Genome-Wide Gene Expression Analysis of Bordetella pertussis Isolates Associated with a Resurgence in Pertussis: Elucidation of Factors Involved in the Increased Fitness of Epidemic Strains. PLoS ONE, 8(6): e66150. doi: 10.1371/journal.pone.0066150

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/23776625
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679012/
• Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0066150
• Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0066150&representation=PDF
• Copyright: © 2013 King 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. (info found here)
• Publisher: PLOS ONE (respected open access organization)
• Availability: online only
• Did LMU pay a fee for this article: no
• Web site where the data resides: EBI ArrayExpress

Hoo, R., Lam, J.H., Huot, L., Pant, A., Li, R., Hot, D., & Alonso, S. (2014). Evidence for a Role of the Polysaccharide Capsule Transport Proteins in Pertussis Pathogenesis. PLoS ONE 2014;9(12):e115243. doi: 10.1371/journal.pone.0115243

• PubMed Abstract: http://www.ncbi.nlm.nih.gov/pubmed/25501560
• PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4264864/
• Publisher Full Text (HTML): http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115243
• Publisher Full Text (PDF): http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0115243&representation=PDF
• Copyright: © 2014 Hoo 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. (info found here)
• Publisher: PLOS ONE (respected open access organization)
• Availability: online only
• Did LMU pay a fee for this article: no
• Web site where the data resides: NCBI GEO

Links

• User Page: Brandon Klein
• Team Page: The Class Whoopers

Assignments Pages

• Week 1 Assignment
• Week 2 Assignment
• Week 3 Assignment
• Week 4 Assignment
• Week 5 Assignment
• Week 6 Assignment
• Week 7 Assignment
• Week 8 Assignment
• Week 9 Assignment
• Week 10 Assignment
• Week 11 Assignment
• Week 12 Assignment
• No Week 13 Assignment
• Week 14 Assignment
• Week 15 Assignment

Individual Journal Entries

• Week 1 Individual Journal
• Week 2 Individual Journal
• Week 3 Individual Journal
• Week 4 Individual Journal
• Week 5 Individual Journal
• Week 6 Individual Journal
• Week 7 Individual Journal
• Week 8 Individual Journal
• Week 9 Individual Journal
• Week 10 Individual Journal
• Week 11 Individual Journal
• Week 12 Individual Journal
• No Week 13 Journal
• Week 14 Individual Journal
• Week 15 Individual Journal

Shared Journal Entries

• Week 1 Class Journal
• Week 2 Class Journal
• Week 3 Class Journal
• Week 4 Class Journal
• Week 5 Class Journal
• Week 6 Class Journal
• Week 7 Class Journal
• Week 8 Class Journal
• Week 9 Class Journal
• Week 10 Team Journal
• Week 11 Team Journal
• Week 12 Team Journal
• No Week 13 Journal
• Week 14 Team Journal
• Week 15 Team Journal