Name ______________________________SEARCHING THE SCIENTIFIC LITERATURE (DUE BEFORE LAB THE WEEK OF FEB 1)Accessing scientific literature is critical to conducting and reporting biological research. This exercise is intended to walk you through the process of finding relevant published material. The specific articles identified, as well as the general approaches, will be of direct relevance to you when you write your first papers and interpret future journal articles. Finding Literature There are several databases that index biological publications. Among the more commonly used is PubMed. PubMed is a database of papers published in (mostly) peer reviewed journals that include papers on biomedical topics (broadly defined) over the past 40 years, and in some cases much earlier. It actually has a much wider coverage, since general-science journals such as Nature, Proceedings of the National Academy of Sciences, and PLOS One are indexed in their entirety. Its entries include titles, authors and abstracts of papers that have been published, and in some cases papers that have successfully passed peer review and are awaiting publication (tagged as “PubMed - in process” or “Epub ahead of print”). It also links to full copies of older articles, and articles from journals for which WSU has an institutional subscription. Note that similar approaches can be used for other databases such as Web of Science.1. Open your browser (e.g. Firefox, Safari, Chrome, Internet Explorer, etc.).2. Go to http://www.pubmed.gov. (This is part of NCBI: http://www.ncbi.nlm.nih.gov/) [from off-campus, use the following for full access to subscribed journals: http://www.systems.wsu.edu/scripts/WSUAll.pl?http://www.pubmed.gov]3. For a simple search, just enter a search term. Since later in the semester we will discuss viruses, including the viruses the infect bacteria, called bacteriophage, perform a PubMed Search for bacteriophage. 4. How many entries appear? ____________What years were the most recent and the earliest published? Recent:_______________ Earliest: _________________ (Hint: you can adjust your search to display by “Most recent” using the pulldown menu in the upper right).5. Select a bacteriophage article that looks interesting. You want to find an article to which you have full access, so look for a tag at the end of entry stating, “Free article” or “Free PMC Article”. When you select an article, a window will open containing the bibliographical details and abstract of the paper. Copy and paste the first sentence of the Abstract and put it here:6. On the right-hand side of the article’s entry, at the top, will be one or more icons indicating that the free text is available, click on one of those icons (they will be different depending on publisher or database hosting the article). This will allow access to a searchable full-text copy of the paper, usually hosted on the publisher’s site. Search the page for bacteriophage (Ctrl F on most browsers). Note that such a link will be present on the pages for all articles marked “Free article.”7. Near the top of this page, usually either at the top or on the right (each journal has a slightly different layout) there should be a link for “Full Text PDF” or something similar. Select this link. Adobe Acrobat Reader will open to display a PDF of the paper, formatted as it appeared in the original journal. Copy and paste the first sentence of the INTRODUCTION of that paper here:8. Return to PubMed.9. To narrow down your search so you don’t have to sift through tens of thousands of articles, you can use more complex searches. PubMed uses quotation marks “ ” to search for strings of text, for example, “nucleic acids” will return only papers that use that string, not any paper that refers to other acids. It also uses several search terms. ‘AND’ is used to find papers that contain all of a list of words (e.g. Microbacterium AND bacteriophage). ‘OR’ is used when a topic may be referred to in multiple ways. If you are interested in studies on cattle, you may wish to search for cow OR cows OR steer OR steers OR bull OR bulls OR cattle, as any of these terms might be used. Note that this search engine does not automatically search for both singular and plural forms – you must specify both. ‘NOT’ is used to eliminate any paper that uses a word in which you are not interested. Be careful with this, as it will exclude papers that include the word anywhere within the text, and may eliminate a relevant paper due to a passing reference to the excluded term. Finally, PubMed can parse complex combinations of these search parameters,using parentheses to group related terms. If you want a paper that addresses the production of nucleic acid chains, you might use a search such as: (DNA OR RNA OR “nucleic acid” OR “nucleic acids”) AND (synthesis OR polymerization).10. How would you phrase a search for an article on the possible use of a combination of steroid hormones with vitamin A to treat melanoma, which is also known as skin cancer?_____________________________________________________________________11. PubMed can serve as a convenient way to locate a specific paper. Look up this specific paper thatdiscussed bacteriophage: Lumactud R, Shen SY, Lau M, Fulthorpe R. Bacterial Endophytes Isolated from Plants in Natural Oil Seep Soils with Chronic Hydrocarbon Contamination. Front Microbiol. 2016 May24;7:755To search for this paper you can enter key words, the entire title, or the names of several authors (note the syntax: surname first, then initials, with commas used to separate authors, thus: Lumactud R, Shen SY...) Find this paper in PubMed. Give the PubMed ID (PMID, the unique identifier in this database, at the bottom of the article’s page) for this paper _______________12. With a citation, you can also access articles directly through the WSU library card catalog. For the article cited in question 11, go to (http://www.wsulibs.wsu.edu/) and in the “SearchIT” searchbox, type the journal’s name (Front Microbiol.). Usually you would select the online version and follow it to the journal’s web site, but the WSU library shows you that this journal is for free on PubMed (and they don’t have it). Using the link that the WSU library gives you for this journal, track down the article, download the PDF of the article on the Microbacterium bacteria and copy and paste the first
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