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BSCI 1510L Literature and Stats Guide: 2.2 Accessing Scientific Papers

Introduction to Biological Sciences lab, first semester

2.2 Accessing Scientific Papers

Historically, looking up a paper at Vanderbilt required a trip to the Stevenson Science Library or Eskind Biomedical Library and a stroll through the rooms full of bound journal volumes.  However, in recent years, journal articles have increasingly become available online and in full text.  So it is becoming rare to have to leave your Internet-connected computer to look up a paper.  There has been strong pressure in the biomedical community to force publishers to make their journals available to the public without cost or access restrictions.  So many papers in biomedically-related fields are accessible to anyone who has an Internet connection and a computer.  In other cases, Vanderbilt has paid for an online institutional subscription (very expensive!!!) to the journal and by recognizing that you are browsing from a computer with a Vanderbilt IP address, you are automatically granted access.  If you are using a non-Vanderbilt IP address and are retrieving a paper through the library website, you may have the opportunity to access the material through a proxy service by entering your VUNET ID.  However, even if you are logged on to the proxy service, there are some resources that may not be available (such as downloads of full-text PDFs) from some providers without an actual Vanderbilt IP address.

In the case where a journal does not have full text access online, you may be able to acquire it in print version.  If one of the Vanderbilt libraries has a subscription to that journal, you will have to make a trip there to look it up in the paper journal.  If Vanderbilt does not have a subscription, the article may have to be obtained from another library through a reciprocal lending agreement or Interlibrary Loan.  However, there are some restrictions on the use of Interlibrary Loan by undergraduates, so it may be easier to just look for another equally relevant paper. 

Like other online resources, Internet-accessible journal articles are retrieved using URLs.  However, these URLs are often not stable, particularly if they result from a search.  It would be possible to try to look for the article through a Google search for the citation of the article.  However, even though the format of a citation is somewhat standardized (i.e. journal name, volume, page numbers), there is a lot of variations on whether the journal name is abbreviated or not, whether the issue number is included, etc.  So this method is often not effective. 

In Sections 2.2.1 through 2.2.4, we will examine several methods for accessing papers online given varying amounts of information about the reference.

2.2.1 Digital Object Identifiers (DOIs)

The publishing community has reached a consensus on a system of identifiers that can uniquely and unambiguously identify articles: digital object identifiers (DOIs).  These identifiers never change and there is a commitment to maintain them long into the future.  Although not all journals are currently assigning DOIs, many are and their use is likely to expand in the future.  If you have the DOI of an article, it is relatively easy to look up the article.

A digital object identifier is written in the form

http://dx.doi.org/xx.xxxx/xxxxxxxxxxx

e.g. 

http://dx.doi.org/10.1007/s11356-011-0632-z 

In some older sources, the DOI is prefixed with "doi:" rather than written as an HTTP URI.  In that case, just replace "doi: " with "http://dx.doi.org/".  To retrieve information about an article, enter the DOI in a web browser.  You should then be redirected to a page which provides information about that article.  Usually at least the abstract is provided and if the article is available as full text, there will be a link to that file or information on how to pay for access.  If you are using a computer with a Vanderbilt IP address, you may be granted access to the article as full text by virtue of a subscription purchased by the library.  In some cases, DOIs have been assigned to articles that are only available in print.  Even in those cases, looking up the DOI should provide information about the article. 

It is now accepted practice to include the DOI at the beginning of the article itself, and at the end of a reference listing for an article if that article has been assigned a DOI.  If you do not know the DOI of an article, you can search for the article using one of the tools described in the next section.

2.2.2 Using the "journal vol:pg1-pg2" reference format to find an article.

If you have a reference that does not include the DOI for the article, you can use the "journal vol:pg1-pg2" information (e.g. "Antimicrobial Agents and Chemotherapy 51:4217-4224") to look up the article.  Go to http://library.vanderbilt.edu/ and select Search Library, Ejournals tab.  Enter the name of the journal.  The search feature may also be able to locate the journal using a standard abbreviation.  If a search using an abbreviation fails it may be because the abbreviation is not standard or unknown to the system.  If you need to look up an abbreviation, you can find a list at http://library.caltech.edu/reference/abbreviations/ .  If Vanderbilt has online access to the journal, click on the "find it @ VU" button.  The resulting window will show the years/volumes to which Vanderbilt has electronic access.  From the link on this page, you will be directed to the journal's website and there you can locate the particular volume and page given in the reference. 

It may be faster to use one of the next two methods, particularly if only part of the information about the article is known (e.g. only the author and year, only the title, etc.).

2.2.3 PubMed and PubMed Central

PubMed and the related PubMed Central (PMC) are important databases which can be used to retrieve articles.  The coverage of these resources is limited primarily to the biomedical literature.  However, there is a significant overlap between the biomedical literature and cell and molecular biology, so they are a useful resource for topics in those areas even if the topic is not strictly medical.  PubMed includes a broader variety of sources, but not all are available in full-text, whereas all resources included in PMC are available in full-text.  So it is advisable to try searching both databases. 

To search these databases, go to the National Center for Biotechnology Information (NCBI) website at http://www.ncbi.nlm.nih.gov (or type http://www.pubmed.gov).  At the top of the page select either PubMed or PMC from the database selection dropdown list.  Then paste some information about the article into the search box and click Search.  Depending on the outcome of the search, you should see either a page about the article or a Results list which will hopefully lead to the article after another click.  Somewhere on the page you should find a "PDF" link to a pdf that you can download or "Free PMC Article" link that will take you to the article.  If the article is not available for free to the public, go to the LinkOut - more resources section at the bottom of the page to try to find a Full Text source for which the Vanderbilt Library has a paid subscription.  If you are looking at the Web version of the article, the Reference section at the end will have hyperlinks to many of the references cited by the paper.

2.2.4 Web of Science

One of the major tools for locating articles in biology is the Web of Science.  It is particularly important when you are looking for papers that are related to a non-biomedical topic of biology.    Web of Science is available from the Vanderbilt Library web page http://library.vanderbilt.edu/ through "Search Library" then the Database tab.  Enter "Web of Science" then click Search.  If you are off-campus, you can click on the login link for access using your VUNET ID and password.  You can select one of the subset databases to restrict your search to a narrower set of journals.  At the search page you can enter terms such as author name and publication year for the article that you are trying to find. 

In the search results, click on the title of the article to go to its page.  From the article page, you can do a number of useful things.  You can:

  • read the abstract of the article.
  • click on the "find it @ VU" button to try to obtain a full-text version
  • obtain the DOI (if there is one)
  • download the reference to a commonly used reference management system (Endnote)
  • find earlier articles that were cited by this article by clicking on the hyperlinked number after "Cited References" on the right side of the page.
  • find later articles that cited this one by clicking on the "view all X citing articles" link.