Skip to main content

BEE 2600: Principles of Biological Engineering (Fall 2017)

Case Study 3 on Isolation of circulating tumor cells in blood

Introduction 

In this tutorial you will learn how to:

  • Find primary scientific information and follow the trail of citations and cited references

  • Search several different specialized databases for primary and secondary information, using both basic and advanced techniques, in order to quickly track which articles and authors are seminal in research area

  • Assess the impact of a given scientific paper and top journals in biological engineering and critically compare and evaluate the information you find from various sources according to specific criteria in order to decide whether or not to include it in your bibliography

Completion of this tutorial is required for receiving full credit on Assignment CS3.

  1. KEEP THIS WINDOW OPEN AT ALL TIMES DURING THE EXERCISE

  2. Some sections have links to videos which will open in a new window. Please make sure you have the latest version of Adobe Flash Player. If a video asks you to save or open it, open it with the latest version of Firefox or IE.

  3. On a Mac, use Firefox or Chrome NOT Safari. Make sure you've enabled Flash. 

  4. See your assignment for due dates.

  5. All instructions needed for successful completion are provided within the tutorial and your assignment.

  6. If you need help with technical issues during the exercise or have questions about the research resources, send an email to Jeremy Cusker or Camille Andrews, your librarians, at jpc27@cornell.edu or ca92@cornell.edu. All other questions about the assignments (e.g., instructions, grades, requirements for satisfactory completion) should be directed to your TA.

Searching for primary literature

Go to Web of Science from the library website. If you need a refresher on how to reach and search these databases, refer to the earlier tutorial or watch this video for tips (06:24).

Web of Science has analytical features that are available in very few other databases that allow you to quickly and easily follow the scholarly conversation on a subject in your field and discover the most highly cited and influential articles, researchers and journals. Because of this Web of Science is a classic standard in the life sciences field.

NOTE: In order to ensure that the "Analyze Results" and "Create Citation Report" options appear, you must be sure you are searching ONLY the Web of Science Core Collection (chosen from the drop-down menu in Web of Knowledge when you begin your search).

 

HINT: You'll notice that most top-cited articles are usually older. This is because the scholarly publication cycle takes so long; it takes awhile for an article to get into circulation and then get cited by other researchers. If you see a relatively recent article with a lot of citations, this is a hot article.

Assessing the Impact of Research

There are other ways to find important authors, institutions, and sources/journals. To do this we'll use the Analyze Results tool in Web of Science.

  • Choose Web of Science Core Collection at the top of the screen BEFORE BEGINNING YOUR SEARCH.

  • Do your search

  • Choose the Analyze Results button at the bottom of the Refine Results toolbar (make sure that you have not hidden it).

  • Choose the criteria you want to analyze by (author, source title, etc) and how many results you want to analyze and click Analyze

  • Check the boxes besides the results you want to view or exclude

  analyzeresults-highlight.png

Watch this video for tips. Please note: though Web of Science has since changed their interface, the database features shown here still function in a similar manner.

HINT: Depending on how you do your search you will get different results on the analysis.

HINT: Modern research is highly collaborative. Some papers may have more listed authors than there are people who will ever read it! The convention in some areas is that the first-listed author in a paper may be either the "primary investigator" OR the head of the laboratory. However in other fields, to help support their graduate students or post-doctoral fellows, the primary investigators may give first author credit to them. Check the affiliations listed below the list of authors. It will often say something about each person's role. If not, doing a web search for the authors can help you discover additional information.

Finding Influential Journals in the Field: Journal Impact Factors

To find out which journals are influential, in Web of Knowledge use Journal Citation Reports and find the Journal Impact Factor.

A journal's impact factor is a "measure of the frequency with which the "average article" in a journal has been cited in a particular year or period". This measure is disputed: it tends to favor review journals but overall it can serve as a general measure of a journal's influence in a field.

HINT: For a more in-depth treatment, see:

Impact Factor (IF) is a rough, quantitative proxy for how influential a given journal is. Very simply, for any given year IF is an average of the number of times articles from a journal were cited over the past 2 years, relative to the number of items published (although it's possible to calculate an IF over any length of time): In a given year, the impact factor of a journal is the average number of citations to those papers that were published during the two preceding years. For example, the 2015 impact factor of a journal would be calculated as follows:

A = the number of times articles published in 2013 and 2014 were cited by indexed journals during 2015

B = the total number of "citable items" published in 2013 and 2014. ("Citable items" are usually articles, reviews, proceedings, or notes; not editorials or letters to the editor.)

2015 impact factor = A/B

To find impact factors:

  • In Web of Knowledge, go to Journal Citation Reports at the top of the page  

 

Link to Journal Citation Reports in top menu bar of Web of Science

You can also reach it from the library website by choosing Databases, typing in Journal Citation Reports, and clicking on the title to enter.

  • Select journals by subject Category and Year. If you're looking for cancer research, you'll need to look for "Oncology." You can see where journals are in relation to the others in that category 

 

‚ÄčIn Web of Knowledge, when you do an article search you can also see a particular journal's impact factor on the right hand side of an article record in the blue section under Additional Information.

Gray Literature

Gray Literature  

Web of Science and other databases we offer all search mostly peer-reviewed, scientific papers. However there are also other types of scientific literature. These include gray literature:

  • government technical reports ("tech reports"),
  • conference proceedings and papers,
  • theses and dissertations, and
  • preprints.

Most of these are considered less prestigious, reliable, and "official" than publication in a peer-reviewed journal. But they are still fully legitimate avenues of publication. Often they are used to publicize early findings, before a study is entirely complete. Or, in the case of theses, they are published as a condition of receiving an advanced degree. Government technical reports are issued either by agencies that do scientific research themselves or else by a lab that has received government funding. Increasingly, such labs may be required to publish technical reports as a condition of receiving such funding.

Gray literature may be cited like any other paper although with the caveat mentioned before that it is considered less "official" and reliable than peer-reviewed scientific papers. There are many sources for gray literature.

Possible sources of gray literature:

 

Evaluating Articles

Evaluating Articles 

Watch this video for tools in Web of Science for evaluating research articles.

Although most peer-reviewed articles have been screened as a part of the publication process, not all articles are created equal. Determining the value of a particular paper or other resource is important. The library has a guide to evaluating sources here.

The main criteria are:

  • Quality & Accuracy: Quite simply, is it good science? Very few scientifically incorrect papers are published and papers with serious scientific errors tend to be noticed right away (that's the purpose of peer review and publication itself). It does happen however. Check for errata, debates in the letters and opinions section, and later research. Also, some papers are much more informative and thorough than others. Some researchers will try and "slice" their research into the smallest possible publishable findings so as to be able to generate multiple papers out of a single study. Others may have issues with their methodology. 

 

  • Authority: It can be risky to generalize, but authors with many publications in a given area are usually older, more experienced, and more knowledgeable about a given research area. In the author affiliation section or by doing a web search for the author, you can often find more information on their education and credentials in the subject area.  

 

  • Quantity of Citations: Papers that are cited more times are said to have had greater impact; other scientists found them more useful. Obviously this will vary for newer versus older papers, which is why you should also consider . . . 

 

  • Currency: Newer findings are generally (but not always) better than old ones. Science and engineering are in a constant process of revision and improvement. Old findings may be perfectly accurate and important, but later research will usually refine and expand upon it.

 

  • Relevance: Don't rely just on keywords or the abstract--read the paper fully if you are trying to decide whether to use it. 

 

  • Limitations of the Search Engine/Database/Index: Never assume that you're "getting everything" when you use an individual database or search tool; there are always limits to coverage regarding subject area, age, international coverage, etc. 

 

  • Journal: Some journals are more prestigious than others, having broader readership and/or more-selective criteria for accepting papers. Publication in a journal like Science orNature usually marks a paper as being exceptionally important. One good way of determining the importance of a given journal is . . .

 

  • Impact Factor: Web of Science, Scifinder and several other databases will all link you the 2-year Impact Factor for the journal of any article you look at: You won't have to calculate it yourself. 

 

  • Point of View or Bias: This can be difficult to determine at first glance but reading an article in comparison to others on the subject, checking the language used and whether the authors address alternate points of view in their literature review, and seeing if the authors disclose their funding sources (as they are required to do) can help.