Accessing Medline- A Workshop in PubMed and Medline-OVIDGroup members: Vivian, Bridget, Ashley,

and Kristen B

Today's Workshop1. Learning Objectives (Kristen)

2. Medline (Kristen)

3. Literature Review (Ashley)

4. PubMed (Bridget)

5. PubMed-NCBI (Bridget)

6. Medline-OVID (Vivian)

7. Medline-OVID - My Workspace (Vivian)

8. Class Activity

Learning Objectives1. Comparison of how MeSH maps natural

language differently between PubMed and Medline- Ovid

2. Understand how to save, share, and combine search strategies and auto-alerts for PubMed and Medline-OVID

3. Understand how to export citations into RefWorks from PubMed and Medline-OVID

Medline

• Premier, comprehensive biomedical database in the United States

• Updated daily

• 5500 biomedicine and life science journals in nearly 40 languages

• English abstracts are including for more than 80% of the records

• Full text coverage: 1948-Present

• Number of records: 18000000+

Literature Review Allison JJ, Kiefe CI, Weissman NW, Carter J, Centor RM. The art and science of searching Medline to answer

clinical questions. Intl J of Technology Assessment in Health Care. 1999; 15 (2): 281-296.

Delwiche, FA. Searching Medline via Pubmed. Clinical Laboratory Science. 2008; 21 (1): 35-41.

De Groote, SL. PubMed, Internet Grateful Med, and Ovid: A comparison of three Medline internet interfaces. Medical Reference Services Quarterly. 2000; 19 (4): 1-13.

Gault LV, Shultz MS, Davies KJ. Variations in medical subject headings (MeSH) mapping: From the natural language of patron terms to the controlled vocabulary of mapped lists. J Med Libr Assoc. 2002; 90 (2): 173-180.

Katchamart W, Faulkner A, Feldman B, Tomlinson G, Bombardier C. PubMed had a higher sensitivity than Ovid-Medline in the search for systematic reviews. J of Clinical Epidemiology. 2011; 64 (7): 805-807.

Thiele RH, Poiro NC, Scalzo DC, Nemergut EC. Speed, accuracy and confidence in Google, Ovid, PubMed, and UpToDate: Results of a randomised trial. Postgrad Med J. 2010; 86: 459-465.

Lit Review Findings • Usability and User Preference of Ovid vs. PubMed

• Effectiveness of search tool dependant on user’s familiarity with it

• Functionality (use of Boolean operators, truncations and proximity searching)

• Variations in how Ovid and PubMed map free language onto MeSH

• Sensitivity of PubMed vs. Ovid in retrieving all relevant articles

• Use of Filters

User PreferenceThiele RH, Poiro NC, Scalzo DC, Nemergut EC. Speed, accuracy and confidence in Google, Ovid, PubMed, and UpToDate: Results of a randomised trial. Postgrad Med J. 2010; 86: 459-465.

Google 45%

PubMed 25%

Ovid 4%

UptoDate 26%

Variations in MeSH Mapping Gault LV, Shultz MS, Davies KJ. Variations in medical subject headings (MeSH) mapping: From the natural language of patron terms to the controlled vocabulary of mapped lists. J Med Libr Assoc. 2002; 90 (2): 173-180.

Cannot assume symmetrical retrieval from MeSH in different systems

Pubmed and Ovid provide methods for suggesting mesh, but methods are varying

SensitivityKatchamart W, Faulkner A, Feldman B, Tomlinson G, Bombardier C. PubMed had a higher sensitivity than Ovid-Medline in the search for systematic reviews. J of Clinical Epidemiology. 2011; 64 (7): 805-807. PubMed has higher sensitivity than Ovid

The Study:

• PubMed found more results for each concept - rheumatoid arthritis, MTX and randomized control trials

• 18 eligible articles were selected, Ovid had 17

Limits and Filters Winchester DE, Bavry AA. Limitations of the MEDLINE database in constructing meta-analyses. Ann Intern Med. 2010; 153: 347-8

• When search limits are used, researchers miss important and relevant records

• Only limits that can be safely used are dates and language – those not based on MeSH

• Applying search limits is not an integral part of search strategy - well executed searches benefit from limits when they are applied post hoc to remove unwanted documents

Tips and Tricks Revealed in Lit Review1. Use both MeSH and free text words to limit Eg. search "trial" as

free-text in the abstract filed in addition to MeSH

1. Use synonyms and truncation

1. Don't actively limit but use double negation Eg. (NOT (Animals [MeSH] NOT Humans [MeSH])) - ensures no non-indexed human studies are missed

1. Use existing methodological filters such as PubMed's Clinical Queries feature where you can choose filters related to clinical trials in addition to free-text and MeSH

PubMed - Introduction • What is PubMed?

• Types of Citations

• Advanced Search Builder

• Automatic Term Mapping

• MeSH Subheadings (Qualifiers)

• Search Field Descriptions & Tags

• Filters

• Features (Single Citation Matcher, Clinical Queries & My NCBI)

• RefWorks Refresher

PubMed - What Is It?

• Free access to MEDLINE

• Links to full-text articles in PubMed Central, publisher web sites, and other related resources

• Over 22 million citations

• Developed & maintained by the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM)

PubMed - Type of Citations

• PubMed - as supplied by publisher

• PubMed - in process

• PudMed - indexed for MEDLINE

• PubMed

• PubMed - OLDMEDLINE

PubMed - Example:

May miss non-indexed papers or "wrongly indexed" papers if only MeSH is used

Use both MeSH terms AND keywords, including synonyms, related terms, variant endings and spellings

PubMed - Comprehensive Searching

PubMed - Advanced Search Builder

•

• Choose a field (if you like)

• Run Search

• Combine search strings

Isolate concepts

PubMed - Automatic Term Mapping (ATM)

• Maps keywords to MeSH headings, journal titles or author names

• Splits phrases apart and searches each term separately and combines them

• Parts of a search can be removed and/or added and rerun

PubMed - Keep in Mind...

•

• PubMed ignores Stopwords (i.e. because, regarding, mostly, however, each, etc.)

List of Stopwords: http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T43/?report=objectonly

Must use UPPERCASE for boolean operators

PubMed - Use with Caution...

•

• Phrase searching is possible with "double quotations"

*Warning: Using truncation or quotations will automatically turn off mapping and MeSH term explosion (try to use in addition by combining with OR)

Use the asterisk* for truncation (limited to first 600 variants of the root)

Use the MeSH database to find a suitable term and "Add to Search Builder", then run your search in PubMed

PubMed - Wrong Term Mapped?

PubMed - MeSH Search Tags (Qualifiers)

[mh] To search a MeSH heading

[majr] To search a MeSH heading that is a major topic of an article

2 Search Field Tags:

PubMed - Warning:

Warning: Using only MeSH subject terms excludes in-process & publisher-supplied citations & others that do not (or do not yet) include MeSH subject terms

PubMed - MeSH Search Tags No Exploding

Turn-off automatic explosion by adding :noexp

i.e. [mh: noexp]

[majr: noexp]

Terms will automatically explode

PubMed - MeSH SubheadingsWant to Get More Specific?Add MeSH

Subheadings (also called Qualifiers) by adding a slash and typing in the Qualifier's name or the Qualifier's abbreviation

i.e.

eye/injuries [majr]

or

eye/in [majr]

*case and spacing don't matter

*cannot turn off the explode feature for a subheading

PubMed - Subheadings cont'dList of Subheadings:

http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T41/

Subheading Definitions: http://www.nlm.nih.gov/mesh/topsubscope.html

Qualifier Hierarchies:

http://www.nlm.nih.gov/mesh/subhierarchy.html

PubMed - Search Field Descriptions/Tags

List of PubMed Data Element Field Descriptions:

http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.T44/?report=objectonly

Limits your search

PubMed - Author Field

•i.e. austin j [au]

• Will automatically truncate. To stop this, add quotations

i.e. "austin je" [au]

Last name followed by a space followed by up to two initials followed by a space and a suffix abbreviation

PubMed - Date Field•

• To search for a specific date, use this format:

YYYY/MM/DD [date field] *month and year are optional

6 different date fields. Most common will be Date of Publication [dp]

PubMed - Date Field cont'd...

Date Field

Date ranges can be entered with a colon

i.e., 2004:2006

Comprehensive searches for a full year

i.e., 2000:2000

(will retrieve citations with a different print and electronic year of publication)

Searching by date FAQ:

http://www.ncbi.nlm.nih.gov/books/NBK3827/#pubmedhelp.Searching_by_date

PubMed - Filters•

• Select filter (left side of screen)

• Click on "Show Additional Filters" if necessary

*Filters will remain for all subsequent searches unless they are cleared

Run a search

PubMed - Single Citation Matcher

•• Enter the information you have to fill in the blanks

• Click go

Click Single Citation Matcher from the PubMed homepage

PubMed - Clinical QueriesA search interface to find citations in the areas of:

• Clinical Study Categories: Find citations corresponding to a specific clinical study category.

• Systematic Reviews: Find citations for systematic reviews, meta-analyses, reviews of clinical trials, evidence-based medicine, consensus development conferences, and guidelines.

• Medical Genetics: Find citations related to various topics in medical genetics.

PubMed - My NCBI

•

• Need to register (free!)

Allows for some function and customization options (User Preferences, Filtering Options, Save Search Strategy or Alert Setup)

PubMed - My NCBI:User PreferencesSome include:

• Link options

• Email options

• Display highlighted terms

• Single Citation Display

PubMed - My NCBI:Filtering Options

•

• Can customize your own filter and name it

Apply up to 5 filters in MyNCBI

PubMed - My NCBI:Save Search Strategy & Alert Setup

• Max number of saved searches is 100 per user-name

• Saved searches cannot be edited

• Limited to one email address per account

*related articles cannot be saved; date and date ranges are not recommended for saved searches

PubMed - RefWorks Refresher

In PubMed...

1) Mark appropriate records in your search

2) Add to Clipboard (from "Send to" menu)

3) Display the Clipboard contents

4) Change "Display Settings" to Medline format

5) Select and Copy all of the text

PubMed - RefWorks Refresher Cont'd

In RefWorks....

6) Select References > Import

7) Select NLM PubMed from the Import Filter drop down menu

8) PubMed will appear automatically as the database

9) Click on the From Text link

10) Paste text into the box

11) Click IMPORT

Medline-OVID

• Uses OvidSP - their flagship research platform

• More than 2500 ebooks and collections, including archive collections of critical historical materials, as well as publisher and topical collections

• Over 1300 premium, peer-reviews journals, including dozens of journal collections

• Over 100 bibliographic and full-text databases

• Disciplines: Medicine, Nursing & Health Professions, Behavioural Sciences, Basic Science, Humanities & Technology

Medline-OVID

Mapping

• OVID uses vocabulary mapping which searches using natural language terminology

• The mapping process uses OVID's statistical algorithm to determine which terms are associated with certain subject headings

• The use of mapping increases a user's retrieval precision

• Ovid will automatically maps search terms to the database's controlled vocabulary

Medline-OVID

Command Line Syntax

• Allows shortcut commands to be added to a user's search, circumventing the use of the icon bar

• Use of command line in OVID overrides MeSH mapping

Examples:

• exp <term> - This command within a controlled vocabulary database would explode the term

• * <term> - This command within a controlled vocabulary database would focus on that term

• <term>.ab. - This command would search term term through the abstract (ab) field of the database

Medline-OVID

Truncation and Wild Cards

• Unlimited truncation - "$" or ":", such as "cancer$" which will retrieve "cancer", along with "cancers" and "cancerous"

• Limited truncation - "$" or ":" paired with a number will retrieve the root word with that maximum number of character, i.e. "dog$1" will retrieve "dog" and "dogs", but not "dogma"

• Mandated Wild Card - "#" is used within or at the end of a term to substitute one required character, i.e. "wom#n" will retrieve "women" and "woman", however "dog#" will retrieve "dogs", but not "dog" because it require another character to be present

• Optional Wild Card - "?", used to substitute one or no characters, useful when dealing with American/British word variants, i.e. "colo?r" will retrieve "color" and "colour", however "?" will not work if there is only one letter before the wild card

Medline-OVIDStopwords

• Words with that hold little value or meaning

• These words are often discarded in a search unless

• Ovid has elimated Stopwords, now user's can search words/phrases such as "is there hope.tw"

Medline-OVIDRefWorks

• Bibliographic information can be exported into RefWorks in Ovid

Medline-OVID - My WorkspaceMy Searches & Alerts•Search strategies/strings can be saved

o Save as Temporary (24hours)o Save as Permanent (valid subscription)o AutoAlert (searches automatically on regular basis and emails the

results)o Expert Searches (An expert creates a search strategy that is

shared and available to allow multiple users to share searches on the same group account)

My eTocs•Email alerts user when the journal they subscribe to updates its table of contents

Class ActivityFollow instructions on your handout and

complete exercises.

If you have any questions, raise your hand and we can help.

Class discussion

MeSH VariationsOvid: Depression (default) but there are other

choices in list

PubMed Automatic Mapping: Depressive disorder OR depression

PubMed Mesh Browser: Depression, depressive disorder and more options

PubMed Mesh Browser or Default Search?• PubMed Browser is more like Ovid - building block

style with user control over which MeSH is selected

• PubMed default automatic mapping is intelligent and handy, but it doesn't always account for all MeSH that could be used but can retrieve more documents...

Choosing how you want to search is up to you! All about user preference, but can't always trust automatic mapping...

Differences in Ovid's MeSH list and PubMed's Browser List Ovid provides shortest list of MeSH choices (average is 8

terms) with a selection rate of 62%

PubMed has a list 3x longer with a selection rate of 63% (Gault et. al)

Not much difference...

In PubMed you have a higher chance of choosing inappropriate term

Combining Concepts and ResultsPubMed MeSH Browser:

((("Depression"[Mesh]) OR "Depressive Disorder"[Mesh]) AND "Mass Screening"[Mesh]) AND "Women"[Mesh]

# of results - 17

PubMed Automatic Mapping:

("depressive disorder"[MeSH Terms] OR ("depressive"[All Fields] AND "disorder"[All Fields]) OR "depressive disorder"[All Fields] OR "depression"[All Fields] OR "depression"[MeSH Terms]) AND ("mass screening"[MeSH Terms] OR ("mass"[All Fields] AND "screening"[All Fields]) OR "mass screening"[All Fields]) AND ("women"[MeSH Terms] OR "women"[All Fields])

# of results - 614 #of results for combined concepts - 8881

Combining Concepts and ResultsOvid (user selection):

Depression and mass screening and women

# of results - 6

Command Line Answer for PubMed Field Descriptor

Question:hepatitis b[mh] AND Murphy TV[au] AND 2012:2013[pd]

Answer for Ovid Dot Commands:hepatitis b. and Murphy TV.au and 2012:2013.yr

OR

hepatitis b. AND Murphy TV.au AND 2012:2013.yr