BIM 116: Writing Assignment #3
Library databases & other resources for BIM 116
(Biomedical Engineering: Physiology for Biomedical Engineers, Fall 2019)
Libraries on Campus:
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.
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).
- MedLine Plus: Health Topics (NLM Consumer Health Information)
Symptoms, causes, treatment and prevention for over 900 diseases, illnesses, and health conditions.
- CDC (Centers for Disease Control) – Diseases and Conditions:
A-Z index of diseases and conditions.
- Online Collections of Medical Texts
Library resources include online collections of medical texts, many include information on diseases. Resources relevant to this assignment are listed below.
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)
- Additional Resources:
Many national organizations, such as those listed below, provide information on diseases in their web pages.
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 is the primary article index for medicine and clinical research.
Coverage: 1946 – present.
Web of Science indexes research in all disciplines, including medicine.
Coverage: 1900 – present.
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.
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)
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
- 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)
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 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
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:
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
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.
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?
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.
To cite your sources correctly, you need to understand:
- How to use “in-text” and “full citations” citations in your academic papers
- What Citation Style to Use
- 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.
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 
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|
|Title of Article||Apoptosis in the pathogenesis and treatment of disease|
|Title of Journal:||Science|
Use “Endnote Online” to put your citations in IEEE Format:
***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)
Export will happen automatically
Select citations to export (use checkboxes)
Click dropdown arrow to the right of SEND TO link (upper right part of screen)
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
File: Enter name of file (e.g., citations.nbib)
Import option: PubMed (NLM)
To: Select group (library) where citations should be imported
3. Create Libraries (two methods)
MANAGE MY GROUPS
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
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
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.
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
• 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).
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 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
- Connected Medical Devices
- Design Controls for the Medical Device Industry
- Guidelines for Failure Modes and Effects Analysis for Medical Devices
- Handbook of Human Factors in Medical Device Design
- ISO 13485:2016: A Complete Guide to Quality Management in the Medical Device Industry
- Medical Device R&D Handbook, Second Edition
- Medical Device Reliability and Associated Areas
- Medical Device Regulatory Practices
- Medical Device Safety: The Regulation of Medical Devices for Public Health and Safety
- Medical Devices and Systems
- MEMS and Nanotechnology-Based Sensors and Devices for Communications, Medical and Aerospace Applications
- Practical Design Control Implementation for Medical Devices
- Reliable Design of Medical Devices
- Usability Testing of Medical Devices
Additional Print & Online Resources:
Print resources are available at the library and call number indicated.
Biomedical Engineering Desk Reference
Shields R856.15 .B56 2009
McGraw Hill’s Access Engineering (via CDL hosted site)
A large collection of engineering handbooks
Try searching for: medical and device
2011-2019: developed, updated, used by C. Craig to teach BIM116