Revision as of 02:21, 10 November 2015

Class Notes

Notes from 11/03/2015

Two papers we need to find:

Genome Sequence Paper
Microarray Data/Paper
- Several requirements for this data to make it work with our project.
- Rank the papers what we want to do 1-8 (2 papers/person)
- Dr. Dahlquist will confirm which paper matches all of our criteria, and we will proceed with that paper.
- Our ELN will include the process that we used to find our papers and the annotated biblio. from our genome paper and the one or two microarray papers.
  - Then we copy our annotated biblios onto the team page and rank the microarray papers

Find LibGuide here.

Notes from 11/05/2015

May be helpful to go to a Microarray Database and search for data on our species and then find corresponding papers.
- Not cut and dry, some data may not have papers linked.
Always used the advanced search - especially on PubMed.
Web of Science has a link called "## Cited References" which, when clicked on, presents a list of links that lead to the articles that the original article references.
Web of Science, like Google Scholar, also has a "Cited By" link that indicates which articles have cited the original article.

Electronic Lab Notebook

Find Genome Paper
- PubMed
  - Searching "Burkholderia cenocepacia genome" returned 150 results.
  - Searching "Burkholderia cenocepacia genome[Title/Abstract]" returned 5 results.
  - Filtering by publication date (last 5 years) returns 3 results.
  - Advanced Search Options:
    - The advanced search options used included requiring the search term to be in the title and abstract and filtering by year.
    - Requiring the search term to be in the title/abstract helped cut down the most number of results. It is incredibly beneficial if the exact topic of the desired paper is known.
- Google Scholar
  - Searching "Burkholderia cenocepacia genome" returned 18,100 results.
  - Filtering by "no patents" returned 17,800 results.
  - Searching "allintitle: Burkholderia cenocepacia genome" with the same filter as above returns 17 results.
  - Advanced Search Options:
    - The advanced search options used included filtering to remove patents from the search results and requiring search terms to be in the title of the articles.
    - Requiring the search term to be in the title/abstract cut down most of the excess search results here. Having the no patent filter is also incredibly helpful in determining whether the results we have are actually journal articles that we want.
- Web of Science
  - Searching "Burkholderia cenocepacia genome" by Topic returned 188 results.
  - Searching "Burkholderia cenocepacia genome" by Title returned 22 results.
  - Searching these results with the term "nucleotide sequence" returned 3 results.
  - The third result is the paper titled "The Genome of Burkholderia cenocepacia J2315, an Epidemic Pathogen of Cystic Fibrosis Patient" that we are using for our project.
- Prospective search in the ISI Web of Science/Knowledge database of genome sequence paper
  - How many articles does this article cite?
    - This article has 150 cited references.
  - How many articles cite this article?
    - This article is cited 128 times in Web of Science Core Collection, and 468 in All Databases.
  - 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?
    - Based on the titles and abstracts of the papers that cite this article, some topics of research include: bacterial antimicrobial metal ion resistance, ffflux pump-mediated drug resistance, biofilm formation in Burkholderia, and the relationship between Burkholderia and Cystic Fibrosis.
  - Advanced Search Options:
    - We searched the key terms in the title fields of the papers, and then refined further using Web of Sciences refining search option.
    - Searching by the title was incredibly helpful to narrow down the number of results we had. That being said, having the refining search tool is a cool way to narrow down search results in a more open ended manner.
Find Microarray Paper
- In ArrayExpress, filtered by organism Burkholderia cenocepacia, experiment type "rna assay", experiment type "array assay".
  - This search resulted in 24 results.
  - In order to find array data with articles, I systematically clicked through all of the experiments in my search results in order of highest to lowest replicates and looked for the experiments with a paper associated or linked.
  - Links to relevant articles from ArrayExpress:
    1. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
      - 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?
      - Is this article available in print or online only?
      - Has LMU paid a subscription or other fee for your access to this article?
    2. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0028831
    3. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0058943
      - 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?
      - Is this article available in print or online only?
      - Has LMU paid a subscription or other fee for your access to this article?

@@ Line 88: / Line 88: @@
-=== 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:
-*# 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 [http://libguides.lmu.edu/c.php?g=324079&p=2174128 Writing LibGuide])  You will be using one of three formats, “journal article from database (with DOI), journal article from database (no DOI) or journal article in print (no DOI).)
-*#** The link to the abstract from  [http://www.ncbi.nlm.nih.gov/pubmed PubMed].
-*#** The link to the full text of the article in [http://www.ncbi.nlm.nih.gov/pmc/ 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 [http://creativecommons.org/ 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 [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.]
-*#** Is this article available in print or online only?
-*#** Has LMU paid a subscription or other fee for your access to this article?
-*# 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?
-*# 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.
-*#** A minimum of three biological replicates need to have been performed for each condition measured (so that we can do statistical analysis of the data).
-*#** The experiment performed is a competitive hybridization (also known as a "two-color" or "two-channel") experiment where one sample was labeled with the Cy3 dye and the other sample was labeled with the Cy5 dye (i.e., not an "Affymetrix" chip).
-*#** The control sample needs to be derived from mRNA and not genomic DNA.
-*#** The gene IDs used on in the data files must match the gene IDs that are cross-referenced by UniProt (Dr. Dahlquist can help with this one).
-*#* 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:
-*#**# 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?
-*#** Remember, microarray data is not centrally located on the web.  Some major sources are:
-*#*** [http://www.ebi.ac.uk/microarray-as/ae/ 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.
-*#*** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO]
-*#*** [http://smd.princeton.edu/ Stanford Microarray Database]
-*#*** [http://puma.princeton.edu/ 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.
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Revision as of 02:21, 10 November 2015

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