BIM 116: Writing Assignment #3

Library databases & other resources for BIM 116
(Biomedical Engineering: Physiology for Biomedical Engineers, Fall 2019)

___________________________________

 

In this Guide:

Libraries on Campus:  

Campus Map

Shields Library is the only library currently open during the Covid Pandemic. For regularly updated information regarding library resources, please look at our Covid Update Page.

If you need any assistance, please feel free to use our Help page or look at our short library tutorials.

 

Resources below provide general information on diseases.

Use them to choose a disease for your assignment, and get basic information on cause(s) and treatment(s).

Access Medicine

Stat!Ref   Note:  in this title “stat” does not refer to statistics – it is the medical term for “urgent” and free registration is required for this resource.

 

First:  search for your disease by name. 
If you get too many hits, try narrowing your search by including the search terms “etiology” (causes) and “epidemiology” (causes, distribution, and control of diseases).  For example: “Name of disease” AND (causes or epidemiology or etiology)

 

Search for additional resources on the web.

 

1.  Find an article database that indexes research in your area.

Subject Guides  list library resources, including article databases, by discipline.  From the Subject Guides page click on the broad area that covers your subject (e.g., Engineering or Physical Sciences)  or scroll down to see the list of subjects (departments).

The best databases for this assignment are:

PubMed

PubMed is the primary article index for medicine and clinical research.
Coverage: 1946 – present.

PubMed Tutorial & Online Training

Web Of Science

Web of Science indexes research in all disciplines, including medicine.

Coverage: 1900 – present.

Web of Science Help


2.  Conduct Your Search:

An outline is given below as a reminder of what we covered in class.  For help with your search,  visit a library reference desk, or use other library help options.

 

PUBMED:
Start with a Keyword search for the name of a disease  (EXAMPLE:  shingles).

Focus your search by adding additional terms to your search, connected with AND:

  • shingles AND causes
  • shingles AND treatment

Click on the LIMITS (Additional Filters) links to the left of your results to restrict your results by:

  • Publication dates
  • Article types  (click on Review)
  • Language(s)

Consider searching the MeSH database (Medical Subject Headings)  for the name of your disease to get more robust results.

  • In the box to the left of the search box, change the default “PubMed” to “MeSH” (by clicking on the dropdown arrow).
  • Enter the name of a disease in the search box and click SEARCH.
  • Click on the result that matches what you are looking for.
  • In the screen that appears, select:
    –EPIDEMIOLOGY (transmission and control of diseases) and
    –ETIOLOGY (causes of diseases) and “Restrict to MeSH Major Topic”.
  • Click on the ADD TO SEARCH BUILDER button (upper right side of screen).
  • Click on the SEARCH PUBMED button after the terms appear in the “PubMed Search Builder” window.

 

Once you know the MeSH terms to add, you can improve the “robustness” of your search, and take a shortcut by adding the appriopriate term after the name of the disease (separated by a slash) at the main search screen.   Adding “treatment” or “causes” after the name of a disease (also separated by a slash) also works.   For example:

  • NAME-OF-DISEASE/epidemiology     e.g., West Nile Fever/epidemiology
  • NAME-OF-DISEASE/etiology             e.g., West Nile Fever/etiology
  • NAME-OF-DISEASE/treatment          e.g., West Nile Fever/treatment
  • NAME-OF-DISEASE/causes               e.g.,  West Nile Fever/causes

 

 


WEB OF SCIENCE:

Start with a TOPIC search for the name of a disease  (EXAMPLE:  shingles or herpes zoster).

Focus your search by adding additional terms to your search, connected with AND:

  • shingles or herpes zoster
  • AND
  • cause* or treatment*

The asterisk is a truncation symbol, so your search will include: cause or causes or causal, etc.)

Too many hits?

  • Limit your search by doing a TITLE search rather than a TOPIC search.  Change the default “TOPIC” to “TITLE” by clicking on the dropdown arrow to the right of the search box.

LIMITS: After conducting your search, use the blue REFINE RESULTS bar to the left to limit your search by:

  • Document Type: select REVIEW
  • Publication Year

Use the SORT BY option in the upper right to sort your articles by times cited:

  • SORT BY:  Times Cited – highest to lowest
  • Highly cited articles generally have a higher impact

Click on the LIMITS link under the search box to limit your search by:

  • type of article:  (limit to review)
  • year(s)
  • language

For additional help with your search, stop by any Library Reference Desk.

 


3.  Get The Articles You Want:     

After you have conducted a search you will see a list of citations.
Use the article abstracts to decide which article(s) you want to get.
Click on the UC-eLinks  or UCD-eLinks  button so see your options for getting a copy of the article.

 

UC-eLinks             UCD-eLinks

 

UC-eLinks      UC-eLinks

UC-eLinks will either take you directly to the online version of the article, or show you the options below (if the article is not online, or if the UC-eLINKS software cannot connect to the article).

Get It Online From:
IF the article is available electronically, you will see this option first. Click on
one of the links under this heading to get an electronic copy of the article (look for the PDF version).

R – E – A – D what the links say to make sure to click on the right one for your article.  Sometimes we buy different years of content from different sources (example: years 1996 to the present will be available through one link; years 1930 – 1995 will be available through another link).   NOTE: If the article is not available electronically, or if UC-eLinks did not get sufficient information from the database to find the an online link, the “Get It Online From” option will not appear.

Find a Copy
If the journal is not available electronically, click on the HARVEST or MELVYL link to see if  it is available in print.  Harvest shows what UC Davis owns.  MELVYL lists was all the UC’s own, and will also search outside the UC system.  If the print journal is available at UC Davis, note the call number, the library where the journal is kept, and the complete citation to the article. Then you can go to that library, locate the journal using the call number, and scan or copy the article.

UC-eLinks also provides links to:
Request this from another library…  Request an article through Interlibrary Loan
Add Citation to a Bibliography
Get Help

 

UCD-eLinks     UCD-eLinks

UCD-eLinks will open the library catalog record for the journal/resource, and list online and/or print options for obtaining the article.  Options are:


View Online
IF the article is available electronically, you will see links for accessing it under this heading.  Click the appropriate link to access.

View Online – Additional Services

IF UC Davis does not subscribe, click

INTERLIBRARY LOAN:  to request it
MELVYL:  to search for it at another UC
REPORT A PROBLEM: to let UCD and UC know of any problems with accessing the resource

 

Send To
Allows you to email, print, or export the citation (not the article) to Endnote, and get to the catalog’s permanent link for journal/resource.

 

Availability
If available in print, the call number and library location will be listed here.  Note the call number, the library where the journal is kept, and the complete citation to the article. Then you can go to that library, locate the journal using the call number, and scan or copy the article.

 


4.  Need More Help?

Visit a library reference desk, or use other library help options.

The librarians working there will be happy to show you how to search a database, or find a journal, or answer any other questions you have.

 

In academic work, it is important to cite your sources anytime you quote or summarize any work that is not created by you. This includes: text, charts, photos, graphs, diagrams, ideas, or anything else that you did not create.

   2 Minute Video:  Avoiding Plagiarism          4 Minute Video:  Tips to Avoid Plagiarism

 

To cite your sources correctly, you need to understand:

  1. How to use “in-text” and “full citations” citations in your academic papers
  2. What Citation Style to Use
  3. Parts of a Citation

 


1. To cite your sources, use “in-text” citations within your paper and “full citations” at the end, using an the appropriate citation style.  The format of both will depend on the Citation Style you use.

 

3.1) Place in-text citations within your paper

Example: In-Text Citations
number format, superscript:

what-you-summarized-or-quoted.1

number format, italics:

what-you-summarized-or-quoted (1).

author-name and date format:

what-you-summarized-or-quoted (Thompson, 1995).

3.2) Place full citations at the end

Example: Full Citations At End

 

 


2. What Citation Style Should I Use?   IEEE Format

Many different Citation Styles exist, print manuals or online sites should be available to explain how to use them.  Use the citation style your professor or TA indicates.  Many citation styles are used in engineering, a safe bet for engineering is the IEEE citation style.   If your professor or TA did not specify a particular Citation Style or Citation Manual, ask them which one to use, or use the library’s “Citation Styles web page”  to select one.

IEEE Citation Format is outlined here:  IEEE Citation Style Guide

From this we can see:

in-text citations should have this format:  what-you-summarized-or-quoted  [1]

full citations for online journal articles should have this format:

Thompson, C. B.  (1995, March). “Apoptosis in the pathogenesis and treatment of disease.” Science. [On-line]. 267(5203): pp. 1456-1462. Available: http://www.jstor.org/stable/pdfplus/2886538.pdf?acceptTC=true [Sept. 23, 2011].

 

Can’t My Computer Do this for me??

Yes. Go to Endnote Online in 5 Easy Steps  section of this page.

Follow the instructions for setting up a Endnote Online account, and exporting citations from Web of Science and PubMed.

Then have Endnote Web put them in IEEE format for you.

 


3. Parts Of A Citation:

Below, I use a citation from the journal Science, to specify the information given in each part of the citation.

C. B. . Thompson. (1995).  Apoptosis in the pathogenesis and treatment of disease. Science. 267(5203), pp. 1456-1462.

Author C. B. Thompson
Year Published 1995
Title of Article Apoptosis in the pathogenesis and treatment of disease
Title of Journal: Science
Volume: 267
Issue: 5203
Pages: 1456-1462

Use “Endnote Online”  to put your citations in IEEE Format:

 

1. Register for an Endnote Online account

***Make sure VPN is on***

Use the link above, or,
From the Web of Science database: click on the “Endnote” link  (in tool bar at top screen)

 

2.  Getting References INTO Endnote

 

From Web of Science:

Log on to Endnote Online
Search Web of Science.  Then from the Web of Science results screen:

Select citations to export,

click on the Save to EndNote online link
choose  Save to EndNote online

Use Numbers of Records to identify which citations to send, then for Record Content  choose:   (Author, Title, Source, and Abstract)
click SEND

Export will happen automatically

 

From PubMed: 

Select citations to export (use checkboxes)
Click dropdown arrow to the right of SEND TO link (upper right part of screen)

Select FILE
Select: FORMAT: MEDLINE (drop down option)
Select: SORT BY: any option is fine

Click CREATE FILE
Choose:  SAVE FILE  (the default name is: pubmed_result.txt)

Log on to Endnote Online
Select COLLECT tab
Select IMPORT REFERENCES
Enter:

File:  Enter name of file  (e.g., citations.nbib)
Import option:  PubMed (NLM)
To:  Select group (library) where citations should be imported

Click IMPORT

 

3.  Create Libraries (two methods)

 

ORGANIZE tab

MANAGE MY GROUPS
New Group

–OR–

MY REFERENCES tab

Select references for new library
ADD TO GROUP –> New Group

 

4.  Getting References OUT of Endnote

To create List of References:

Select  FORMAT tab
Select BIBLIOGRAPHY

References: choose library
Bibliographic Style: choose citation style
File Format: choose RTF

Choose:  SAVE, EMAIL or Preview & Print

Cite While You Write

Let’s you embed citations in your Word document, while using Endnote Online to format them

 

 

5.  Sharing References

Allows you to share references with others

ORGANIZE tab
Manage My Groups
Manage Sharing:   Add email(s)

 



CITE WHILE YOU WRITE:  How to Use Endnote Web for In-text Citations

The Cite While You Write (CWYW) feature in Endnote and Endnote online allows you to create in-text citations and full citations at the end of your paper.

See the video below for instructions on how to install the CWYW Plugin, and use this feature.

The chart below indicates minutes:seconds on the 8 minute video for each relevant topic.

min:sec              Topic                                                                                    

1:55                        How Install Cite While You Write Plug-in

2:50                       How to Choose the proper citation style:  Choose IEEE

If you don’t see IEEE format, go to Endnote Online:

Under top tool bar: FORMAT –> Bibliography –> SELECT FAVORITES: and add it here.

3:40-on                 Using Cite While You Write for in-text citations and full citations at end of paper

 

 

Working with Endnote Online:  Cite While You Write

 


ENDNOTE — For info on the client/desktop version, see:   Endnote: Getting Started Guide


 

Impact Factor:

• Is a number used to indicate how influential, or important a particular journal is

• Impact Factor refers to a journal, not to an article, and not to an author (although publishing an article in a journal with a high impact factor is generally considered prestigious)

• The benefits and pitfalls of impact factors are a widely discussed topic in academia. Others measures exist to evaluate the influence of journals, articles, and authors.

• Developed in the 1950’s by Eugene Garfield, Institute of Scientific Information (ISI)

 

How To Find a Journal’s Impact Factor:

1. From the Library Databases Page select Journal Citation Reports (aka: JCR, and InCites Journal Citation Reports).
From Library Home Page –> Databases  –> Enter “Journal Citation Reports”
Or from Web of Science, click  “Journal Citation Reports”.

2. To find Impact Factor for a journal:

o Enter the name of the journal or click the BROWSE BY JOURNAL box  (then enter journal name)
o On the JOURNAL PROFILE, the most recent Impact factor is in box below on the right, calculation info is directly below

o Unless your assignment specifies otherwise, use the the most recent year available
(because of what is needed to calculate impact factor, the most recent year is the previous year)

 

How Impact Factors Are Calculated:

2005 Impact Factor for Journal X = A / B, where:

A = Number of times articles published in Journal X in 2003-2004 were cited by indexed journals in 2005

B = Number of articles published in Journal X in 2003-2004

 

Things to be aware of:

• “indexed journals” means journals indexed by the producer of the Web of Science database (Clarivate Analytics). If  Web of Science doesn’t index the journal, it doesn’t get included.

• “number of articles” Web of Science also decides what counts as an “article” (or “citable item”). Usually included are: articles, communications, reviews, notes, etc. Excluded are “news” type items, letters to the editor, etc.

• The lower the denominator, the higher the impact factor.

• A journal’s impact factor refers to a certain year: impact factors do vary from year to year, although most established journals tend to have fairly consistent impact factors (i.e., they don’t vary widely).

 

 

 

Several options for finding background information on authors are listed below.

 

1.  Use Web of Science or PubMed to conduct an author search to determine:

  • How many articles have they published?
  • What institution(s) are they affiliated with?

 

2.  Use Web of Science to:

 

a)  Find out how many times their articles have been cited: 

Conduct an author search in Web of Science (or: for the paper of interest: click on the title, then click on each author’s name to seach for their papers)

On the search results page:

Look at the “TIMES CITED“ information given directly under the citation

Sort by  “TIMES CITED”  (upper right)  to see the author’s most cited publications

 

b)  Get the H-index for the author:

The h-index one method for measuring an author’s productivity (there are many!!).

An h-index of 5:  means the author has written 5 papers that have been cited at least 5 times

An h-index of 50:  means the author has written 50 papers that have been cited at least 50 times

 

How to get the H-index:

After conducting an author search in Web of Science:

Click on “Create Citation Report” link in the upper right.

Web of Science will calculate the h-index for you, it is given on the page that appears (right of the graphs).

 

For more information on the h-index, see:

H-Index help link from WOS

Nature paper on H-indexNature 436, 900 (18 August 2005)

Paragraph explaining h-index from Nature paper above:

“The h-index is the highest number of papers a scientist has that have each received at least that number of citations. Thus, someone with an h-index of 50 has written 50 papers that have each had at least 50 citations. This, says Hirsch, is fairer than alternative measures based on publication. Counting total papers, for example, could reward those with many mediocre publications, whereas just counting highest-ranked papers may not recognize a large and consistent body of work.”

 

3.  Search Google Scholar  to find out if they have a Google Scholar Profile: 

 

Google Scholar profiles:

  • compile a list of a researcher’s publications
  • list citations to those publications
    • (Web of Science and other databases also do this, citation metrics DO differ, this is a significant issue in academia
    • calculate metrics such as:  h-index, i10-index, etc.
  • calculate metrics such as:  h-index, i10-index, etc
  • are available to anyone who wants to establish one
  • typically only used by reseachers (scientists, university faculty, etc.)

 

  • NOTE:  h-index from Google Scholar and Web of Science differ – you need to:
    • report the source of your information
      • h-index according to Google Scholar for NAME on DATE, was:  STATE VALUE
      • h-index according to Web of Science for NAME on DATE, was:  STATE VALUE
    • understand why the values differ: because they use different data to make the calculations (WOS: uses articles indexed in their database; Google uses whatever they index on the web (which they do not disclose))

 

Below are online books and other resoureces that provide information on medical devices.

For more assistance, stop by the PSE Library Reference Desk or the HSL Library Reference Desk.

 

CRCNetBase (Taylor & Francis):

CRCNetBase is an collection of online handbooks in engineering.

The titles below will come up when you enter this search:     “medical device*”

  • Try additional searches for:  
    • the name of a specific medical device  
    • for example:  prosthesis,  pacemaker,  cardiac valve, stent

 

 Additional Print & Online Resources:

Print resources are available at the library and call number indicated.

Biomedical engineering handbook, 2015

Biomedical Engineering Desk Reference
Shields R856.15 .B56 2009

Biomedical Technology and Devices handbook, 2004

Standard handbook of biomedical engineering and design 2003

 

McGraw Hill’s Access Engineering    (via CDL hosted site)

A large collection of engineering handbooks

Try searching for:  medical and device

 



Guide Background:

2011-2019: developed, updated, used by C. Craig to teach BIM116