PUBMED: BASIC AND ADVANCED SEARCHING

Nele Pauwels - Information specialist KCGG - nele.pauwels@ugent.be – 09/332.24.43

AIMS

PubMed: workshop basic and advanced searching

1. How does PubMed translates your search terms?

2. What is the difference between PubMed and MEDLINE?

3. MeSH terms: what are they, where can I find them, how and when can I use them?

4. How can I have ensure that I get more focused results?

5. How can I prepare a search strategy for a systematic review?

PUBMED

EXAMPLES

Research question: is physiotherapy

effective in the treatment of

osteoarthritis of the hip?

Search terms: osteoarthritis

PubMed translation:

"osteoarthritis"[MeSH Terms] OR

"osteoarthritis"[All Fields]

[MeSH Terms]

[All Fields]

EXAMPLES

Research question: is physiotherapy effective in the treatment of osteoarthritis of the hip?

Search terms: physiotherapy osteoarthritis

PubMed translation: ("osteoarthritis"[MeSHTerms] OR "osteoarthritis"[All Fields]) AND ("physical therapy modalities"[MeSH Terms] OR ("physical"[All Fields] AND "therapy"[All Fields] AND "modalities"[All Fields]) OR "physical therapy modalities"[All Fields] OR "physiotherapy"[All Fields])

[MeSH Terms]

[All Fields]

EXAMPLES

Research question: is physiotherapy effective in the treatment of osteoarthritis of the hip?

Search terms: physiotherapy osteoarthritis hip

PubMed translation: ("osteoarthritis"[MeSH Terms] OR "osteoarthritis"[All Fields]) AND ("physical therapy modalities"[MeSH Terms] OR ("physical"[All Fields] AND "therapy"[All Fields] AND "modalities"[All Fields]) OR "physical therapy modalities"[All Fields] OR "physiotherapy"[All Fields]) AND ("osteoarthritis, hip"[MeSH Terms] OR ("osteoarthritis"[All Fields] AND "hip"[All Fields]) OR "hip osteoarthritis"[All Fields] OR ("osteoarthritis"[All Fields] AND "hip"[All Fields]) OR "osteoarthritis hip"[All Fields])

[MeSH Terms]

[All Fields]

EXAMPLES

Search term: DCD

(referring to Developmental Coordination

Disorder)

PubMed translation:

"dicarboxydine"[Supplementary Concept] OR

"dicarboxydine"[All Fields] OR "dcd"[All Fields]

EXAMPLES

Search term: elderly

PubMed translation: "aged"[MeSH Terms] OR "aged"[All Fields] OR "elderly"[All Fields]

=> Results includes references with the description ‘xxx aged xxx years’

EXAMPLES

Search terms: self harm PubMed translation (± a year ago):

"dicarboxydine"[Supplementary Concept] OR "dicarboxydine"[All Fields] OR "dcd"[All Fields]

Current PubMed translation: "self-injurious behavior"[MeSHTerms] OR ("self-injurious"[All Fields] AND "behavior"[All Fields]) OR "self-injurious behavior"[All Fields] OR ("self"[All Fields] AND "harm"[All Fields]) OR "self harm"[All Fields]

EXAMPLES

Search terms: prophylactic intervention

PubMed translation: ("condoms"[MeSH Terms] OR "condoms"[All Fields] OR "prophylactic"[All

Fields]) AND ("methods"[MeSH Terms] OR "methods"[All Fields] OR "intervention"[All Fields])

EXAMPLES

Search term: AIDS

PubMed translation: "acquired immunodeficiency syndrome"[MeSH Terms] OR ("acquired"[All Fields]

AND "immunodeficiency"[All Fields] AND "syndrome"[All Fields]) OR "acquired immunodeficiency

syndrome"[All Fields] OR "aids"[All Fields]

=> Results include for example ‘handicapped aids’, ‘visual aids’ and ‘diabetes aids’

EXAMPLES

Search terms: Hypotension blood donation

PubMed translation: ("hypotension"[MeSH Terms] OR "hypotension"[All Fields]) AND ("blood

donors"[MeSH Terms] OR ("blood"[All Fields] AND "donors"[All Fields]) OR "blood donors"[All Fields]

OR ("blood"[All Fields] AND "donation"[All Fields]) OR "blood donation"[All Fields])

=> Results includes references describing ‘blood pressure’ and ‘liver donors’

EXAMPLES

Search term: Parkinson

Vertaling PubMed: parkinson[All Fields]

=> Results including Parkinson as author

EXAMPLES

Search terms: measurement instruments

PubMed translation: ("Measurement

(Lond)"[Journal] OR "measurement"[All Fields]

OR "Measurement ( Mahwah N J)"[Journal] OR

"measurement"[All Fields]) AND

("instrumentation"[Subheading] OR

"instrumentation"[All Fields] OR

"instruments"[All Fields])

APPROACH FOR STANDARD SEARCHES (≠ SYSTEMATIC REVIEW)

Enter Search term(s) in PubMed

Evaluate translated search strategy via Search Details (cf. Automatic Term Mapping)

Start screening / reading the results Correct the search strategy Fine-tune your search strategy

BOOLEAN OPERATORS: AND, OR, NOT / AND NOT

Boolean operators depend on the database

Examples

hip AND arthritis: this search would only retrieve results including both

the words hip and arthritis

osteoarthritis OR osteoarthrosis: this search would retrieve results with

osteoarthritis, with osteoarthrosis acid and with both terms

osteoarthritis NOT knee: this search would retrieve results with

osteoarthritis, and exclude those with knee

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WORKSHOP (1.1 – 1.4)

CONTENT

1. What is PubMed?

2. Access to PubMed (cf. SFX)

3. Indexing

4. Interesting functionalities in PubMed

5. Optimization of your search strategy (cf. sensitivity and specificity)

6. FAQs

Export to EndNote

myNCBI

1. WHAT IS PUBMED?

WHAT IS PUBMED?

PubMed = Public Access to MEDLINE

Content:

‘Indexed for MEDLINE’

‘PubMed - in process’: waiting to be indexed with MeSH-termen (MeSH = Medical Subject Heading)

‘PubMed - as supplied by publisher’: no indexing

Via PubMed.gov

MEDLINEPubMed (not

[yet] indexed for MEDLINE

Search via MeSH terms and free text words

PubMed

Owner National Library of Medicine (US)

Content Scientific articles; articles in press; e-books

Assets - Free access to abstracts (for everybody)- MeSH terms are assigned based on the full text (on 2 levels)

Minor points - American focus- Assigning MeSH terms takes time (everage 6 months)

Free access to full text? PubMed Central (PMC, a database integrated in PubMed)

Unique records (compared to other biomedical databases)? Yes

Indexering/Thesaurus MeSH – updated annually

Filter options Yes (but have limitations!)

Export to Reference Manager Software (e.g. EndNote) Yes

E-mail alerting/RSS Feed Yes

Tools to find relevant search terms External: GoPubMed ; PubReMiner ; MeSHonDemand

See FAQs

2. ACCESS TO PUBMED

ACCESS TO PUBMEDUGhent / UZ Ghent netwerk AND access via

www.kcgg.be or via lib.ugent.be

=> SFX button full tekst availability via Ghent

University

Access PubMed directly: https://www.ncbi.nlm.nih.gov/pubmed

Access PubMed via the KCGG website: https://www.ncbi.nlm.nih.gov/pubmed?otool=ibeuglib

ACCESS TO PUBMEDUGhent / UZ Ghent netwerk AND access via

www.kcgg.be or via lib.ugent.be

=> SFX button full tekst availability via Ghent

University

3. INDEXING

INDEXERING IN PUBMED

Publication

National Library of Medicine

Indexing- MeSH / Major Topic- Subheadings

INDEXING:EXAMPLE

* = MeSH Major TopicMeshterm/subheading

VOORBEELD MESH TERM EN SUBHEADINGS

MeSH term

Subheadings

Exclude Child Terms -> Specificity ↑

Restrict to Major Topic -> Specificity ↑

Synonyms -> Sensitivity ↑

Nitrofurantoin was added as MeSH term to this article But this term was not mentioned in the abstract

Without including the MeSH term, you would not have found the article...

Nitrofurantoin was neither added as MeSH term (althought the article has been indexed yet), neither mentioned as such in the abstract. The synonym ‘furadantin’ was mentioned in the abstract.

Without including synonyms, you would not have found the article...

WORKSHOP (2.1 – 2.4)

4. FUNCTIONALITIES IN PUBMED

Based on predefined search filters e.g. to search for certain publication types (e.g. systematic reviews) or topics (e.g. AIDS).

Evaluate the Search Details when using thePubMed filters!

WORKSHOP (3.1 – 3.4)

5. OPTIMIZE YOUR SEARCH STRATEGY

SEARCH TIPS AND OPERATORS IN PUBMED

PubMedBoolean operators AND, OR and NOT (AND is the default setting)

Attitional tip: use round brackes to separate between different operators e.g. (xxx OR xxxx OR xx) AND xxxx

Truncation operators * multiple characters will be automatically added at the end of a word e.g. Heart attack* Pay attention: this operator can not be used in combination with dubble quotation marksPay attention: when > 600 combinations => PubMed will limit to the first 600 combinations (check Search details)

Proximity opertors -

To search for a particular combination of therms (Phrase searching)

Dubble quotation marksExample: “heart failure”!!!: Automatic Term Mapping is desactivated (= MeSH terms will not be automatically added. The ‘phrase’ will be searched in All Fields)

Or

Add field code such as [TIAB]

Search in tite, abstract and author keywords

[TIAB]

Search in the list of MeSH terms [Mesh]: Child terms will be included[Mesh:NoExp]: Child terms will not be included in the search

38

WORKSHOP (4.1 – 4.4)

SPECIFICITY VS. SENSITIVITY

SPECIFICITY OF YOUR SEARCH STRATEGY ↑

Use MeSH Major Topic (syntax [Majr])

Use subheadings

Restrict to MeSH term itself [parent term], without including the ‘child terms’

Add topic-specfic search blocks via the PubMed homepagina

Apply filters

E.g. article type

E.g. species, age groups, gender

E.g. date of publication (see ‘Results by Year’)

Via the MeSH database

By using the filter options on the left side of the results page(be carefull – see next slide !)

SEARCH FILTERS IN PUBMED: REASONS TO BE CRITICAL / CAREFULL

Article type e.g. Clinical trial => AND clinicaltrial[ptyp] But, a lot of publications don’t have a publication type assigned But, no consistency (e.g. Multicentre study)

Species e.g. Human => AND humans[MeSH] But, not all articles have been indexed (yet) It is better to use: NOT (animals[MeSH] NOT humans[MeSH])

Ages e.g. Birth – 18 years => AND ("infant"[MeSH Terms] OR "child"[MeSH Terms] OR "adolescent"[MeSH Terms])) But, not all articles have been indexed (yet) or a such (e.g. pediatric, boy, toddler, etc.) It is better to use a validated search filter for ‘Children’

Gender e.g. Female => AND female[MeSH] But, not all articles have been indexed (yet)

SENSITIVITY OF YOUR SEARCH STRATEGY ↑

Use MeSH term (syntax [MeSH]) instead of MeSH Major Topic

Do not use subheadings (unless as floating subheading e.g. rehabilitaton[subheading])

Included the MeSH term(s) as free textword(s) into your search strategy

Add synonyms as free text words into your search strategy

Source of inspiration in PubMed: Entry terms

External sources of inspriation who use PubMed content: GoPubMed ; PubReMiner ;

MeSHonDemand

Additional external source: synonymes and PICO search module in Embase

WORKSHOP (5.1 – 5.2)

6. FREQUENTLY ASKED QUESTIONS

IMPORT REFERENCES INTO ENDNOTE ≤ 200 references: Send to > Citation Manager

> 200 references

‒ Send to > File: select MEDLINE as format. A txt-file will be generated.

‒ In EndNote: Via Import > Select the txt-file and select

‒ ‘PubMed (NLM)’ as Import Option

46

MYNCBI & E-MAIL ALERT

To save searches

To save search strategies

To personalise home page (e.g. highlight your search terms in the results)

To receive an e-mail alert with new results - based on your search string - are available

=> Login required (free)

myNCBI

Best Match = sort by option

Results based on frequency count of search terms

MeSH terms are not taken into account

Number of results may change !

Intended goal: to screen the 1st resultspage

TAKE HOME MESSAGES

APPROACH FOR STANDARD SEARCHES

Search term(s) in PubMed

Evaluate translated search strategy via Search Details (cf. Automated Term Mapping)

Start screening / reading the results Correct the search strategy Fine-tune your search strategy

Take home message

Search for appropriate MeSH terms Select relevant fields codes (e.g. [TIAB]) for appropriate free text words

Add syntax (e.g. double quotation marks)

ONLINE SUPPORT

Information sheets of KCGG

Link to Tutorial provided by the supplier

Courseshttp://www.kcgg.ugent.be/events/

KCGG.UGent

@kcgg2

Ghent University

Nele PauwelsInformation specialist

GE55 – KNOWLEDGE CENTRE FOR HEALTH GHENT (KCGG)

CAMPUS UZ GHENT - K3 GROUND FLOOR (ENTRANCE 42)

E nele.pauwels@ugent.be

T +32 9 332 24 43

www.kcgg.ugent.be