Difference between revisions of "Dwilliams Week 10 assignment"

Revision as of 17:18, 31 October 2013

Electronic Journal Week 10

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. Glenn Johnson-Grau will be giving a guest presentation in class on Tuesday, October 29 to introduce you to searching various bibliographic databases.

• 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.)
     • State which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). :Used PubMed
     • State what you used as search terms (e.g., "genome") and what type of search terms (e.g., keyword, author, title, etc.): Search terms used were (Chlamydia trachomatis[MeSH Terms]) AND Genome[Title]
     • Give an overview of the results of the search.
       • How many results did you get? :9 Results
       • Give an assessment of how relevant the results were.: Most of the results were very relevant.
     • Record the full bibliographic citation of the relevant paper(s), formatted according to the Guidelines for Literature Citations in a Scientific Paper.
     • Create a link to the HTML version of your journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
     • Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.
  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 results did you get?
       • 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 two potential journal articles that refer to public microarray data for your species than are different than what your teammates have found. Thus, each team should find either 6 (for a 3-person team) or 8 (for a 4 person team) articles. If you cannot find all six or eight 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.
     • State which database you used (e.g., GoogleScholar, PubMed, ISI Web of Science/Knowledge). It may actually be easier to find the microarray data first and then find the corresponding journal 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.
     • Record the full bibliographic citation of the relevant papers, formatted according to the Guidelines for Literature Citations in a Scientific Paper.
     • Create a link to the HTML version of the journal article on the publisher web site. Note that PubMed Central is not an actual publisher web site, but a secondary database of papers.
     • Download the PDF file of the journal article, upload it to the wiki and link to it from your team's home page. Note that you can only upload the PDF file to our wiki if there are no copyright restrictions on the article. If there are copyright restrictions, then you will need to provide a link to the download on the publisher site.
     • You must also link to the web site where the microarray data resides.
     • Download the microarray dataset file, upload it to the wiki, and link to it on your individual and team pages.
       • Remeber, microarray data is not centrally located on the web. Some major sources are:
         • NCBI GEO
         • EBI ArrayExpress
         • 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.
       • 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?
     • On your team wiki page, compile the list of citations, links, and answers to questions, ranking the papers one through six (or 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.