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Internal Medicine Residents & Students: 3 Accounts for Research, PubMed Tutorials, Search Optimization

Guide for teaching Internal Medicine Residents

3 Necessary Accounts for Research

Register for three accounts that will help you in research -

 

1. ILLIAD - for interlibrary loans of articles that are not available as full text electronically or in print at LHS. LHS delivery is rapid and you may have your article as soon as 1-2 days!

Sign up at:  https://proxy.cc.uic.edu/login?url=https://uic.illiad.oclc.org/illiad/illiad.dll

You will need your I-Card number, which starts with 28198 or 20111 - you only need to fill out the first page - don't worry about the account information page.

 

 

2. RefWorks - the citation management database can be accessed online from anywhere. 

a. Sign-up at: https://www.refworks.com/refworks2/default.aspx?r=authentication::init&groupcode=RWUIllChicago

The RefWorks Group Code may be needed for when you working off campus.   You will need to login with your NETID and password to get the group code.


b. Familiarize yourself with the RefWork's tutorials page at LHS  http://researchguides.uic.edu/content.php?pid=74619&sid=552483

These tutorials are well worth the time and provide an introduction to the many time-saving features associated with using RefWorks to manage your citations and write your papers using Write-N-Cite.

c. Next, view an introductory video on RefWorks at UIC (this is the first tutorial on the guide) https://www.youtube.com/watch?v=QcDdiI6mUyY&feature=youtu.be


 

3. MYNCBI - PubMed's online bibliographic management system and more - use it to save collections, searches, bibliographies....

a. Sign-up at:   https://www.ncbi.nlm.nih.gov/account/?

 

 b. Watch the tutorial on MYNCBI  for an Overview http://www.youtube.com/watch?v=ks46w3mNAQE

 

 

 

The "Find It @ UIC" Button - How to Access Full-text

    

1. a. Read about the "Find It @ UIC" button.

The "Find it @ UIC" button only appears if you have entered the database (e.g., PubMed) via the LHS library gateway. This button links you to the electronic full-text of an article if it is available. When you begin your database search via the LHS webpages, look for this icon in your search results! If you are in PubMed and do not see this button, you probably did not enter PubMed through the LHS website.

If the article is not available electronically through the library's subscriptions, you will  be presented with this message - "Article is not available in electronic format." 

To request a scan of a full-text article via interlilbrary loan, scroll down the page to ILLIAD's link "Library of the Health Sciences Chicago and Distance Ed"

The information required to process the interlibrary loan should populate the form automatically if you access ILLIAD from the Distance Ed link. 

Interlibrary loan often takes as little as 1-2 days. A message is sent to your UIC email that your article has arrived. Login to ILLIAD at https://uic.illiad.oclc.org/illiad/IAX/illiad.dll?Action=99.-- After logging into ILLIAD, look on the left-sidebar look for the link labelled "Electronically Received Articles."

 

2. a. Watch a brief video, in which Ryan Rafferty demonstrates the use of the "Find it @ UIC" button and ILLIAD in the context of PubMed search  http://www.uic.edu/depts/lib/lhs/resources/guides/pubmed/searching_pubmed_2_demo.htm

 

b. Watch a brief video, in which Rebecca Raszewski demonstrates the ILLIAD registration, the "Find It @ UIC" button, and the interlibrary loan process in the context of a CINAHL database search http://www.uic.edu/depts/lib/lhsc/demos/CINAHL/articles_need_ordering.swf

 

What are Boolean Operators?


Boolean Operators are words used in searching databases to control how sets of results are/or are not combined. Boolean Operators include

AND        OR       NOT

The Boolean operator -  AND -  intersects concept sets, returning search results that reflect articles which address both concepts. If AND is used, then any article which addresses only one concept will not be included in the search results.

The Boolean operator  - OR  -  unifies concept sets, returning search results that include articles if at least one concept is present. The Boolean operator  - OR - will always expand search results.

The Boolean operator  - NOT  - will exclude articles if the NOT concept is present - do not use the NOT operator without giving it great thought because it is easy to "throw the baby out with the bath water" - in other words, to inadvertently discard articles you may want to look at because the NOT concept term is incidentally present and mixed in with concepts you do want to retrieve.   

 

View the following tutorial by the USF Polytechnic Library, which relies on visualizations to introduce simple and complex usage of Boolean Operators: http://www.youtube.com/watch?v=i1LpTbzSKd0

 

View Emily Mazure's tutorial, which quickly introduces you to the uses of Boolean Operators in searching: http://www.youtube.com/watch?v=ffw70AU9pc0

 

 

MEDLINE/PubMed Resources Guide Page

PubMed Tutorials - Exercises 12 -13

12. The  5 Tips for Searching PubMed tutorial by Duke University Medical Center Library demonstrates a patient safety topic search in PubMed - https://www.youtube.com/watch?v=6wWeeCBBlk4

This tutorial explores the patient safety search using 3 key concepts –

1) Health care workers   2) Influenza vaccine   3) Patient infection

Sign in to your MYNCBI account. Return to the PubMed homepage.  Please duplicate the Duke search in PubMed by following all of the steps in the tutorial exactly as shown - this is a challenge. Show your work via snip/screenshots in your Assignment Document.

Begin by finding the PubMed home screen through the LHS Library website http://researchguides.uic.edu/c.php?g=252191  - scroll down under Research Databases until you find PubMed. Consider bookmarking the LHS Medicine homepage.

After completing the 3 separate searches for Health care workers, Influenza vaccine, and Infection (you will need to copy the Duke modification of the Health care worker term from the tutorial), go to the Advanced page using the Advanced link under the PubMed search box. Create a search that intersects all 3 concepts (use AND to join the concepts together in an intersecting relationship). Show a snip/screenshot of your work from the Advanced page with the combined 3-concept search.

Currently, the search recreation should bring you about 202 search results. Write the librarian if you are struggling with this. Also, an easy way to get it right is to make a snip of the screen that shows you Duke's Advanced search page - then you can see exactly how they did it.  

 

13, View this tutorial for directions on using Filters and the Advanced page to complete the additional exercises: PubMed Advanced Search by the University of Michigan Library https://www.youtube.com/watch?v=vtjrN752Occ

On the search results page for the combined search above, use the following filters to modify the search – English language, last 10 years, randomized controlled trials. You will have to use the “Customize” and “Show additional filters” links to see some of these filters before you can select and apply them. Remember that the filter is not applied until you see the blue checkmark. The search results are finally reduced to about 3 citations once all the filters have been added. Show your work with a snip/screenshot.

Moving Citations, Creating Collections, Saving Searches

MYNCBI TUTORIALS - Very Brief!

MeSH Tutorial -   https://www.youtube.com/watch?v=uyF8uQY9wys

Using Filters for PubMed Searching -  https://www.youtube.com/watch?v=696R9GbOyvA

Saving COLLECTIONShttps://www.youtube.com/watch?v=iXSttEKntCE   (Note, if the Favorites icon does not show on the citation page, use the pull-down menu at Save Items).    

Create Alerts (Save SEARCHES for future use as filters) -  https://www.youtube.com/watch?v=WbFjV91YNNY

Keyword Searching (Details box, Advanced page)  -    https://www.youtube.com/watch?v=eEY1r_GDzcg

Advanced Search Page - https://www.youtube.com/watch?v=dncRQ1cobdc

 

WRITTEN INSTRUCTIONS 

COLLECTIONS in MYNCBI - create a new collection or move new citations to an existing collection -

  1. Click the MYNCBI link to open to your MYNCBI account page (upper right corner of PubMed page)
  2. Select the search you want from the Recent Activity box
  3. On the search results page that appears, check the citations you want to move (or don't check any to capture the first 1000)
  4. Use the Send To pulldown menu to select Collections > press Add to Collections
  5. Either choose a new collection and give it a new name or use an existing one > then Save
  6. Check out the options on the Managing Collections link.

CREATE ALERT / SAVE SEARCH - to save a search string and schedule e-mail updates -

  1. Select the Search from you MYNCBI home page Recent Activity box
  2. On the search results page, select the CREATE ALERT link (immediately under the search box) > name it  & save it>
  3. Confirm its entry into your MYNCBI saved searches box
  4. Check out the options on the Managing Saved Searches link.

CLIPBOARD - to place selected citations on an 8-hour clipboard associated with your IP address. This Clipboard can be edited, sent on to Collections, moved to RefWorks, or emailed.

  1. Simply select individual citations from the PubMed search results page or to send a large batch of all results (select nothing and the first 500 results will be used)
  2. Click the Send To pulldown menu to select Clipboard > press Add to Clipboard

 

REFWORKS - transfer citations from MYNCBI or PubMed to Refworks

  1. Open your RefWorks account by signing in at http://www.uic.edu/depts/lib/resources/refworks/
  2. Either select your citations from the PubMed search results page or the Clipboard
  3. Click the Send To pulldown menu to select FILE > Select MEDLINE format (this is the tagged format recognized by RefWorks*) - note that if you do not select the citations, you may create an enormous file!
  4. After selecting Create File, look for the pop-up asking about opening or saving the "pubmed_result.txt file"
  5. Open & save or save the file directly to your Desktop (you may rename it)
  6. Go to RefWorks and select the REFERENCES pulldown menu and choose IMPORT
  7. When the popup window appears, make sure you have NLM PUBMED (Import filter/Data Source) and PUBMED (Database) and the correct FOLDER in Refworks you want to use (name a new one or use one already there)
  8. Browse your desktop for the save pubmed_result.txt file and Open it > then press IMPORT
  9. Verify your citations made it to the FOLDER you wanted (you don't want to keep them in the LAST IMPORTED folder because it is overwritten each time you do an new import)

 Link to the UIC REFWORKS tutorial and citation management guides! http://researchguides.uic.edu/content.php?pid=74619&sid=552483

 

Simple search for Case Studies

PUBMED (via the UIC LHS Chicago Gateway so that you are connected to all the proxy server identifications needed to access full text)

  • Enter into the PUBMED search box: sepsis AND encephalopathy
  • From the left-column, in the filters section, select "more" under Article Types - when the menu selection popup box appears, deselect everything except Case Reports and press Show
  • Once the menu selection box disappears, click on Case Reports so that a check mark appears next to the term (indicating the activation of this Case Reports filter)
  • Your search results are automatically filtered for those documents that are Case Reports (this is indicated by a reduction in the Results number)

 

Clinical Queries - Optimizing Searches With Filters

Clinical Queries - CQ is a valuable PubMed search interface that brings specialized filters to aid you in getting the highest levels of evidence for your patient oriented questions. An efficient way to search for answers to clinical questions is to identify when a key point of care resource such as DynaMed or UpToDate last reviewed a topic (and the age of the most central studies on which recommendations are based) and then customize your Clinical Queries search in relationship to that timeframe. 

You can reach Clinical Queries from the PubMed entry page menu. You can simply enter a search string in natural language if you know that your terms will map to MeSH headings as well as keyword terms. If you are in the area of an evolving topic that has not been established in the MeSH vocabulary for a significant period of time, then you may want to make your search string more comprehensive. Once the search results are back, select the type of question (e.g., therapy, diagnosis, etiology, prognosis, clinical prediction guidelines), and whether you want a broad or narrow filter. Note the link to the Haynes search filters at the bottom of the first column results to understand the sensitivity and specificity associated with each of the search filters broad/narrow dimensions. Select the link to the search results at the bottom of the first column to have your search registered in the MYNCBI home recent searches table.

TUTORIAL: https://www.youtube.com/watch?v=yWy0ssLC-ME

Special Topics - Optimizing Searches With Filters

PubMed has developed topic and subject filters that can enable robust searches in specific topics. These filters are helpful because it is difficult to identify all of the relevant terminology for a search each and every time. Although these filters are a great starting point, please don't assume that you cannot improve them. You can! You can also edit and customize them - adding and subtracting terms strategically for your particular search.

If you run the search using the subset field tag (e.g., survivors AND cancer[sb]), you will not see real underlying search string. To see the pre-fabricated search, select the link for the topic and drill down. The cancer search sting is several pages long!

On the PubMed Special Queries page, take a look at the Healthy People 2020 link. On the Healthy People 2020 Structured Evidence Queries page, select the link for Maternal, Infant, and Child Health.  There are 33 searches on a variety of topics of interest to Pediatricians and Neonatalists.

A Strong Search - Tips

  1. Use a word document to develop your search strings so that you can edit it easily.
  2. Search by both MeSH and Keywords. MeSH will bring you the indexed literature, which is important because you cannot think of all the possible terms used for a concept. Keywords will bring you the un-indexed literature, which includes the most current publications (awaiting indexing) and literature that will never be indexed.
  3. Keywords are a way to capture articles which must be identified by new jargon or emerging concept language that has not yet been assimilated into the MeSH vocabulary. Keywords help you capture the cutting edge or latest study.
  4. As you find relevant articles, look to see how they are indexed and include any new MeSH terms in your ongoing search string development.    Include new jargon and keywords as well. Look at the related citations in the right hand column of any good article in PubMed. Then, look at how the article was indexed to enrich your citation string. This is called “harvesting” search terms.
  5. Look at the entry date of a MeSH term to the database. Patient Safety did not become a MeSH term until 2012. If you search for patient safety articles using only the MeSH term, you will not retrieve decades of prior research that was not indexed with the MeSH term.
  6. Look at the search details box and decide if a phrase is being split and does not need to be. It may be better to search for “Patient Safety”[all fields] by itself rather than allow the search translator add into the string the split phrase (patient AND safety). But, reconsider the effects of making this change to the translation if you are in a comprehensive review search.
  7. Use the minimum number of concepts needed to identify your intended literature.  If you are using more than 2 concept searches together, consider whether you are missing anything by including the third, fourth, or other concept search terms in your string. Try different combinations of search terms. Consider whether a search concept is likely to be in the indexing or abstract of all the articles you are seeking -- could the concept exist inside the title/article, perhaps in a table or sub-group analysis. Many things can exist inside a full-text article, but not be accounted for in the title/abstract or indexing. Just because an indexing term exists does not mean the indexer used it. Often, less is more - so put your strategic thinking cap on!  
  8. Search each concept separately and then join them together on the Advanced page since you may want to amplify overly simple concept searches as you discover additional keywords. Join synonyms for the same concept together with OR to create a concept set
  9. Use the subheadings or MeSH Major focus selections judiciously. These selections are available inside a terms MeSH record. Sometimes the indexer does not apply the emphatic Major indexing. In a comprehensive review, you seldom want to insist on a Major indexing term. Similarly, the indexer may not have addressed the subheadings rigorously and if you insist on them in the search, you will lose articles that may be valuable.
  10. Before you create a complex string, see if there is a good systematic review available in your topic area. Look at the review’s search method (often in an appendix) and borrow the search strategy. You might even improve on it. If the review search is fairly recent, you can pick up your search at the point the authors stopped theirs (this is not the same as the article’s publication date but the end date mentioned in the methods section). It is always easier to update a good review and look for more current high level evidence than to recreate the historical record.
  11. Use the Clinical Queries filters, limit by dates, ..add filters to reduce the research results. Clinical Queries utilizes special filters developed by Dr. Haynes that allow you to maximize specificity or sensitivity by question type. Remember, unless a filter is critical, specifying it may reduce results in unanticipated ways - e.g., if the indexer neglected to add "Human" as a MeSH term.
  12. You can also look at the articles cited by or citing your prize article. This puts you in touch with the researchers who may be on the same investigative thread.

Exercise 14

Please follow the steps exactly in this exercise. You will be able to judge the correctness of your follow up by the results answers given at each step. Your aim is to duplicate these results exactly. 

Remember that when you use the left-column filters in PubMed, sometimes a two-step process is required. For example, when choosing an Article Types filter, first you request to see the filters by pressing More under the Article Types section heading, then you select whatever article type you do want to see. Once the article type appears on the filter list, you have the option to select it. A check mark should then appear to indicate that this filter is set.

a. Enter PubMed via the LHS gateway and sign into your MYNCBI account.

b. In the search box, enter the following search string into the PubMed search box:  ("2010/01/01"[Date - Completion] : "2014/05/19"[Date - Completion]) AND (patient safety and communication)  Your results should be about 2,417 results.

c. Go to the Ages filter section. and select More. When the filters menu appears, select 80 and over: 80+ years

Your results should now be 89

d. Return to the Article Types filters and press More. Select the Comparative Study box and Show. When the Comparative Study option appears, select it.

Your results should now be 9

e. At the bottom of the column, select the Show Additional Filters link. Select Journal Categories and press Show. Select the Nursing Journals filter in the Journal Categories section.

Your results should now be 2. The PMIDs of the remaining articles are   22271215  and  19773144

f. Go to the Clear All link and select it.

Your results should now be 2,417 as before!

g. Under the PubMed search box, select the Advanced link. This link will show you the recent search history. Note, this history from the Advanced page is temporary. It follows the IP address of the physical computer and browser - it lasts 8 hours only.

Find the search with 89 results and select the number link itself. You should land back on the results page. Note, the age filter 80+ is applied to this set.  Now, select Core Clinical Journals from the appropriate filter section.

Your results should now be 6.

h. Select Evaluation Studies from the Article Types Filters. (Remember select the More link and select the Evaluation Studies box, then press Show. Next, select this link and verify it by the check next to the study type).

Your results should now be 1.

i. Remember to Clear All your filters again!

 

Once you have completed steps a-i above - Using the Advanced page link (beneath the search box), go to recent search history and show a snip/screenshot of the searches above into your Assignment Document. If you have extra searches in the box, you can delete them by selecting the Search # (see the search column on the Advanced page) and choosing the Delete from History link. This is useful for cleaning up your record.