Advanced PubMed searching

ADVANCED PUBMEDSEARCHINGMarisa Conte

meese@umich.edu

Topics

• Clinical queries and other tools• Search construction: controlled vocabulary and Boolean

searching• Advanced search and limits• Managing results: export citations, save searches and

collections, customize retrieval

Tour

Clinical queries

Special queries and subjects

Single citation matcher

Search construction• Identify relevant concepts, including controlled vocabulary• Combine concepts w/ appropriate Boolean logic• Use special features or limits to refine results

IDENTIFYING CONCEPTSMedical Subject Headings (MeSH)

Search construction: Concept building

• Identify major concepts• Identify preferred terms for concepts (including

subheadings if relevant)• Identify synonyms for major concepts

Review: Keywords vs. controlled vocabulary

Keywords

Controlled

vocabularies

Search construction: Vocabulary

Keywords

Controlled

vocabularies

What are they? Literal search Looks for occurrences of words

When to use? Current topics Difficult-to-describe concepts No vocabulary exists in database

Examples Drug names (Lipitor, Prozac) Slang Concepts (Swine flu, oil spill)

Search construction: Vocabulary

Keywords

Controlled

vocabularies

What are they? Set of words or phrases used to

describe concepts Dictionary of accepted terms for a

database

When to use? Searching a database that uses one

Examples MeSH (Medical Subject Headings) EMTREE (Embase)

MeSH entry - pathology

Subheading: pathology

Shortcuts to MeSH• ‘Search details’ from results screen• View MeSH indexing from relevant citations• Use Advanced search > ‘Search builder’ feature with MeSH

dropdown selected

Identify MeSH terms: Use ‘Search details’

Details

ID MeSH: Citation indexing

Identify MeSH: Search builder

Searching MeSH from PubMed

MeSH database• Identify MeSH headings • Entry terms can suggest keywords for comprehensive

searches• Hierarchy view can help identify more relevant

(broader/more focused) terms• Subheadings can help refine search

• Focus on specific application of MeSH: eg bronchiolitis/drug therapy

• Search builder exports MeSH term to PubMed

Question 1:• Does Epstein Barr virus cause a chronic hepatitis, in

particular one that resembles autoimmune hepatitis?

• Try: keyword search

• Try: Clinical queries, using etiology as a filter

• Try: MeSH (+/- keywords)• Epstein-Barr virus infections [mh] AND hepatitis, autoimmune [mh]

Results 1

COMBINING CONCEPTS

Review: Boolean Logic

Concept 1

Child

Children

Adolescent

Teenager

Concept 2

Obesity

Obese

Overweight

BMI

Concept 3

Mortality

Premature deathAND ANDOR

OR

OR

OR

OR

OR

OR

Combining concepts - searchline• Use parentheses to group related concepts• Capitalize Boolean operators

Combining concepts – search builder

Combining concepts – search history

Question 2• What are the cytologic features that distinguish a high

grade intraductal pancreatic mucinous neoplasm (IPMN) from a low grade neoplasm?

• Identify key terms: intraductal papillary mucinous neoplasm [tiab]; carcinoma, pancreatic ductal [mh]; cytodiagnosis [mh]; cytology [tiab] OR cytologic [tiab]

• Combine concepts

REFINING RESULTS

What do I do when I get …

Too many results?

• Use MeSH and/or subheadings to refine concept definition

• Restrict keywords to title and/or abstract

• Use limits – date, publication type, etc.

• Use special features – clinical queries or topic-specific queries

Not enough results?

• Remove limits• Add keywords or MeSH

terms to improve recall• Use related citations to

identify other relevant concepts

Search construction: Techniques• Limits – use sparingly (language, age, publication type)

Clipboard

Clipboard

MANAGING RESULTSMyNCBI

Set up account• Click myNCBI in upper right corner• Click ‘Register for an account’• Complete registration screen (including email address)• Confirm email sent to account

My NCBI homepage

MANAGE RESULTSEmail, export to EndNote, save as Collection

SAVE SEARCH, SET SEARCH ALERTSSave search URL, save search to MyNCBI

Save search via link

Save search from history

SET PREFERENCES AND FILTERSCustomize PubMed

Setting preferences

PubMed filters

QUESTIONS?meese@umich.edu