PubMed for Trainers Winter 2015 U.S. National Library of
Medicine (NLM) and NLM Training Center PubMed Nuts and Bolts
Slide 2
Goals Revised January 2015 Locate details and history about the
information included in MEDLINE/PubMed records and Search the
fields of MEDLINE/PubMed records efficiently.
Slide 3
Objectives Revised January 2015 After this session participants
will be able to use: the MEDLINE/PubMed Data Element (Field)
Descriptions to find details about the MEDLINE data the search tags
table in PubMed Help to find searchable fields and learn how to
search those fields the Advanced Search page Search Builder to
explore PubMeds indexes the NLM Catalog Journal search to find
journals and build journal sets for searching in PubMed History to
combine searches
Slide 4
The point of the following slides: Revised January 2015
MEDLINE/PubMed data structure can vary by field MEDLINE/PubMed data
inclusion has varied over time PubMed indexing can vary by field
BUT you can search easily because there are tools at your disposal
to: Get details about MEDLINE/PubMed data View PubMed indexing
Shortcut to the data you need
Slide 5
Part I: The Data Revised January 2015
Slide 6
PMID 23082700 TITLEEosinophils in the gastrointestinal tract
AUTHORStraumann A LANGUAGEEnglish SOURCEActa Gastroenterol Belg.
2012 Sep;75(3):310-5 PMID 23029718 TITLEChanging antimicrobial
resistance pattern AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc
Physicians India. 2012 May;60:27-8, 33 PMID 23033785 TITLEGut
bacteria and antimicrobial resistance AUTHORKanerva M
LANGUAGEFinnish SOURCEDuodecim. 2012;128(17):1755-61. Records
Fields Revised January 2015
Slide 7
PMID- 22068643 OWN - NLM STAT- MEDLINE DA - 20111109 DCOM-
20120309 IS - 1438-8812 (Electronic) IS - 0013-726X (Linking) VI -
43 Suppl 2 UCTN DP - 2011 TI - Eosinophilic enteritis presenting as
a perforated duodenal ulcer. PG - E358-9 LID -
10.1055/s-0030-1256526 [doi] AD - Department of Internal Medicine,
King Fahad Specialist Hospital, Dammam, Saudi Arabia.
[email protected] FAU - Issa, H AU - Issa H FAU - Bseiso, B AU
- Bseiso B FAU - Al-Salem, A H AU - Al-Salem AH LA - eng PT - Case
Reports PT - Journal Article DEP - 20111108 PL - Germany TA -
Endoscopy JT - Endoscopy JID - 0215166 RN - Eosinophilic
enteropathy SB - IM MH - Adult MH - Duodenal
Ulcer/complications/*etiology/surgery MH -
Enteritis/*complications/*diagnosis/drug therapy MH -
Eosinophilia/*complications/*diagnosis/drug therapy MH -
Gastritis/*complications/*diagnosis/drug therapy MH - Humans MH -
Intestinal Obstruction/*etiology/therapy MH - Male MH - Peptic
Ulcer Perforation/*etiology/surgery EDAT- 2011/11/10 06:00 MHDA-
2012/03/10 06:00 CRDT- 2011/11/10 06:00 PHST- 2011/11/08 [epublish]
AID - 10.1055/s-0030-1256526 [doi] PST - ppublish SO - Endoscopy.
2011;43 Suppl 2 UCTN:E358-9. Epub 2011 Nov 8. Revised January 2015
MEDLINE format with field labels (Tags)
Slide 8
Data structure varies by field Revised January 2015 Highly
Structured: Author [au] or Grant [gr] or Date fields vs. NOT
structured OR standardized Affiliation [ad] vs. Sometimes partially
structured Abstract [ab]
Slide 9
Highly-structured MEDLINE field examples Revised January 2015
Author [au]Format:Lastname initials suffix Examples:AU Smith AB 3
rd AU McCrary SV Date fields [edat], [mhda], etc. Format:YYYY/MM/DD
HH:MM Examples:EDAT 2003/01/02 04:00 MHDA 2005/08/03 09:00 Grant
Number [gr] Format:Number/code/agency/country Examples: GR
LM0577/LM/NLM NIH HHS/United States GR 058423/Wellcome Trust/United
Kingdom
Slide 10
An unstructured MEDLINE field example: Affiliation [ad] Revised
January 2015
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Over time, MEDLINE data inclusion has varied Revised January
2015 Author policy New fields: Full author name (2002-) Grant
number (1981-) Location Identifier (2008-) Old fields (no new
data): Gene Symbol (1991-1995) Number of References (-2010)
Slide 12
Exercise: MEDLINE/PubMed Elements (the data) Revised January
2015 Explore the MEDLINE/PubMed Data Element (Field)
DescriptionsMEDLINE/PubMed Data Element (Field) Descriptions 1.
Google MEDLINE 2. Go to MEDLINE/PubMed Resources Guide 3. Under
Data Structure, choose Detailed Field/Data Element Descriptions 4.
Look at the author policy 5. Compare these two records: PMID
10595696 and PMID 10595696 PMID 22922874
Slide 13
Part II: Indexing Revised January 2015
Slide 14
PMID 23029718 TITLEChanging antimicrobial resistance pattern
AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India. 2012
May;60:27-8, 33 PMID 23033785 TITLEGut bacteria and antimicrobial
resistance AUTHORKanerva M LANGUAGEFinnish SOURCEDuodecim.
2012;128(17):1755-61. AUTHOR INDEX Jain23029718 Jain S23029718
Kanerva23033785 Kanerva M23033785 TITLE INDEX antimicrobial23029718
23033785 antimicrobial resistance23029718 23033785 bacteria23033785
changing23029718 gut23033785 gut bacteria23033785 pattern23029718
resistance23029718 23033785 Indexes Records Revised January
2015
Slide 15
TITLE INDEX antimicrobial23029718 23029713 antimicrobial
resistance23029718 changing23029718 eosinophils23082700
gastrointestinal23082700 gastrointestinal tract23082700
pattern23029718 resistance23029718 Search Tags antimicrobial [ti]
PMID 23029718 TITLEChanging antimicrobial resistance pattern
AUTHORJain S LANGUAGEEnglish SOURCEJ Assoc Physicians India. 2012
May;60:27-8, 33 PMID 23029713 TITLEAntimicrobial resistance in the
ICU AUTHORSoman R LANGUAGEEnglish SOURCEJ Assoc Physicians India.
2012 May;60:9. Revised January 2015
Slide 16
Search Tags Revised January 2015 Search specific PubMed fields
using tags Syntax is term [tag] Warning! Using search tags turns
off Automatic Term Mapping (ATM)
Slide 17
Search Tags (Look in PubMed Help) Revised January 2015
Slide 18
Article Title [ti] Revised January 2015 [ti] can be used to
search for words and phrases in the title field NOT for the entire
title
Slide 19
Journal Title [ta] Revised January 2015 [ta] can be used to
search for the exact title or MEDLINE title abbreviation NOT for
extracted words or phrases
Slide 20
TITLE INDEX antimicrobial23029718 23082700 antimicrobial
resistance23029718 changing23029718 eosinophils23082700 ABSTRACT
INDEX achievement23029718 acinetobacter 23029718 aeruginosa23029718
amikacin23029718 changing23029718 eosinophils23082700
TITLE/ABSTRACT INDEX achievement23029718 23082700 acinetobacter
23029718 aeruginosa23029718 amikacin23029718 antimicrobial23029718
23082700 antimicrobial resistance23029718 changing23029718
eosinophils23082700 Combined Index Revised January 2015
Slide 21
Title/Abstract [tiab] Revised January 2015 [tiab] finds words
and numbers included in the title, abstract, and other abstract of
a citation. [tiab] is often used by searchers to find topic-related
keywords, BUT: [tiab] does NOT find terms from the subject fields
of PubMed records.
Slide 22
Text word Revised January 2015 [tw] includes: Title Abstract
MeSH headings & subheadings Publication Types Other Terms field
Corporate Author Comment/Correction Notes Chemical Names of
Substances Secondary Source Identifier Personal Name as
Subject
Slide 23
Building Phrase Indexes in PubMed Revised January 2015 A speech
analyzer identifies new noun phrases from the title and abstract
fields of PubMed The phrase is added if it: occurs at least 3 times
in the database contains at least 1 alphabetic character has at
most 6 words Phrases are added to the PubMed indexes twice per
month
Slide 24
Explore the Indexes Searchable indexes are accessible from the
Search Builder on the PubMed Advanced Search page. Revised January
2015
Slide 25
Explore the Indexes (continued) Revised January 2015
Slide 26
Exercise: PubMed Indexes Revised January 2015 Using only the
Show Index feature of the PubMed Advanced Search Builder, answer
the following questions: 1. How many PubMed records are for
articles in the Esperanto language? 2. Is the phrase finger to nose
indexed in PubMed?
Slide 27
Part III: The Tools Revised January 2015
Slide 28
Part III: The Tools Revised January 2015 Previously covered:
MEDLINE/PubMed Elements Page Table of Search Tags in Help Index on
Advanced Search Builder Next up: NLM Catalog Journal Search Search
History features
Slide 29
NLM Catalog Journal Search Revised January 2015
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PubMed Search Results: All citations from the International
Journal of Oncology Revised January 2015
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Broad Subject Terms Revised January 2015
Slide 35
Find related data Revised January 2015
Slide 36
Combining searches in History Revised January 2015
Slide 37
Combining searches in History (cont.) Revised January 2015
Slide 38
Combining searches in History (cont.)
Slide 39
Exercise Revised January 2015 1. Use the NLM Catalog Journal
Broad Subject Terms to find MEDLINE journals about audiology. 2.
Search for all citations in PubMed from these audiology journals.
3. Using History, combine the audiology journal search with a
search for cochlear implants. 4. Limit your search to those that
are included in the Systematic Reviews subset.
Slide 40
Summary Revised January 2015 After this session participants
will be able to use: the MEDLINE/PubMed Data Element (Field)
Descriptions to find details about the MEDLINE data the search tags
table in PubMed Help to find searchable fields and learn how to
search those fields the Advanced Search page Search Builder to
explore PubMeds indexes the NLM Catalog Journal search to find
journals and build journal sets for searching in PubMed History to
combine searches