Enhancing Your PubMed Searching Skills
Resource Packet
2nd Wisconsin Health Information Outreach Summit
August 16, 2005
Green Bay, WI
Additional links to resources:
PubMed Trifolds:
PubMed Basics
http://nnlm.gov/training/resources/pmtri.pdf
PubMed My NCBI
http://nnlm.gov/training/resources/myncbitri.pdf
Searching PubMed with MeSH
http://nnlm.gov/training/resources/meshtri.pdf
PubMed Tutorial
http://www.nlm.nih.gov/bsd/disted/pubmed.html
Non-English Guides to PubMed® Resources
http://nnlm.gov/gmr/training/databases/intlresources.html
(this) Advanced PubMed Searching Resource Packet
http://nnlm.gov/gmr/training/pubmedpacket.doc
MeSH® Subheadings and Related Abbreviations
AB
AD
AE
AG
AA
AN
AH
AI
BI
BS
BL
CF
CS
CI
CH
CL
CO
CN
CT
CY
DF
DI
DU
DH
DE
DT
EC
ED
EM
EN
EP
ES
EH
ET
GE
GD
HI
IM
IN
IR
IS
IP
Abnormalities
Administration and Dosage
Adverse Effects
Agonists
Analogs and Derivatives
Analysis
Anatomy and Histology
Antagonists and Inhibitors
Biosynthesis
Blood Supply
Blood
Cerebrospinal Fluid
Chemical Synthesis
Chemically Induced
Chemistry
Classification
Complications
Congenital
Contraindications
Cytology
Deficiency
Diagnosis
Diagnostic Use
Diet Therapy
Drug Effects
Drug Therapy
Economics
Education
Embryology
Enzymology
Epidemiology
Ethics
Ethnology
Etiology
Genetics
Growth and Development
History
Immunology
Injuries
Innervation
Instrumentation
Isolation and Purification
LJ
MA
ME
MT
MI
MO
NU
OG
PS
PY
PA
PK
PD
PH
PP
PO
PC
PX
RE
RA
RI
RT
RH
SC
SE
ST
SN
SD
SU
TU
TH
TO
TM
TR
TD
US
UL
UR
UT
VE
VI
Legislation and Jurisprudence
Manpower
Metabolism
Methods
Microbiology
Mortality
Nursing
Organization and Administration
Parasitology
Pathogenicity
Pathology
Pharmacokinetics
Pharmacology
Physiology
Physiopathology
Poisoning
Prevention and Control
Psychology
Radiation Effects
Radiography
Radionuclide Imaging
Radiotherapy
Rehabilitation
Secondary
Secretion
Standards
Statistics and Numerical Data
Supply and Distribution
Surgery
Therapeutic Use
Therapy
Toxicity
Transmission
Transplantation
Trends
Ultrasonography
Ultrastructure
Urine
Utilization
Veterinary
Virology
Available by searching the PubMed Help manual for Subheadings; in the Appendices, Table 5;
or go directly to:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.table.pubmedhelp.T40
National Library of Medicine Resources
Updated: 7/17/06
PubMed® Qualifier Hierarchies / Families of Subheading Explosions
(Searching on these subheadings searches the narrower subheadings as well.
Not all subheadings are available for all MeSH® terms.)
adverse effects
poisoning
toxicity
analysis
blood
cerebrospinal fluid
isolation & purification
urine
anatomy & histology
blood supply
cytology
pathology
ultrastructure
embryology
abnormalities
innervation
chemistry
agonists
analogs & derivatives
antagonists & inhibitors
chemical synthesis
complications
secondary
cytology
pathology
ultrastructure
diagnosis
pathology
radiography
radionuclide imaging
ultrasonography
embryology
abnormalities
epidemiology
ethnology
mortality
etiology
chemically induced
complications
secondary
congenital
embryology
genetics
immunology
microbiology
virology
parasitology
transmission
metabolism
biosynthesis
blood
cerebrospinal fluid
deficiency
enzymology
pharmacokinetics
urine
physiology
genetics
growth & development
immunology
metabolism
biosynthesis
blood
cerebrospinal fluid
deficiency
enzymology
pharmacokinetics
urine
physiopathology
secretion
statistics & numerical data
epidemiology
ethnology
mortality
supply & distribution
utilization
microbiology
virology
surgery
transplantation
organization & administration
economics
legislation & jurisprudence
manpower
standards
supply & distribution
trends
utilization
therapeutic use
administration & dosage
adverse effects
contraindications
poisoning
pharmacology
administration & dosage
adverse effects
poisoning
toxicity
agonists
antagonists & inhibitors
contraindications
diagnostic use
pharmacokinetics
therapy
diet therapy
drug therapy
nursing
prevention & control
radiotherapy
rehabilitation
surgery
transplantation
Additional subheadings: classification, drug effects, education, ethics, history, injuries,
instrumentation, methods, pathogenicity, psychology, radiation effects, veterinary
Available at: http://www.nlm.nih.gov/mesh/subhierarchy2006.html with links to definitions.
National Library of Medicine Resources
Updated: 7/17/06
PubMed® Subset Codes
Citation Status Subsets
publisher [sb]
in process [sb]
medline [sb]
pubmednotmedline [sb]
oldmedline [sb]
pubstatusnihms
PubMed - as supplied by publisher
PubMed - in process
PubMed - indexed for MEDLINE
PubMed - processed, but not indexed for MEDLINE
PubMed - OLDMEDLINE for Pre1966
PubMed - author manuscript in PMC
Table 3. PubMed Citation Status Subsets
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.table.pubmedhelp.T38
Topic Subsets
aids [sb]
bioethics [sb]
cancer [sb]
cam [sb]
history [sb]
space [sb]
systematic [sb]
tox [sb]
AIDS
Bioethics
Cancer
Complementary and Alternative Medicine
History of Medicine
Space Life Sciences
Systematic Reviews
Toxicology
Searching PubMed – Subsets – Topics
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Searching_PubMed#pubmedhelp.Topics
Journal Subsets
For the following, use jsubsetname without the [sb]
AIM
D
E
H
IM
K
N
Q
S
T
X
Abridged Index Medicus is a list created 20 years ago of 120 core clinical English language
journals that corresponds to "Core clinical journals" subset in Limits.
Dentistry journals
Citations from bioethics journals or selected bioethics citations from other journals
Health administration journals, non-Index Medicus
Index Medicus journals
Consumer health journals, non-Index Medicus
Nursing journals
History of medicine journals and selected citations from other journals
Citations from space life sciences journals and selected space life sciences citations from
other journals
Health technology assessment journals, non-Index Medicus
AIDS/HIV journals (selected citations from other journals 1980-2000)
Table 2. Journal/Citation Subsets
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.table.pubmedhelp.T37
Other Selected Subsets
free full text [sb]
pubmed pmc local[sb]
pubstatusaheadofprint
all [sb]
loall [sb]
loprovmedlib [sb]
Free full text
Free full-text article available in PubMed Central
Articles that appear on the Web in advance of the journal issue's release
All citations in PubMed
All LinkOut links
LinkOut holdings in this medical library
Box 1. Search Field Descriptions and Tags – Subsets [SB]
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.box.pubmedhelp.Box_1_Search_Field_D#pubmedhelp.Filter_FILTER_SB
and Searching PubMed – Subsets
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.section.pubmedhelp.Searching_PubMed#pubmedhelp.Subsets
National Library of Medicine Resources
Updated: 7/17/06
PubMed®
Publication Types
Addresses
Lectures
Bibliography
Biography
Case Reports
Classical Article (for republished seminal articles)
Clinical Conference (for reports of clinical case
conferences only)
Clinical Trial (includes all types and phases of clinical
trials)
Clinical Trial, phase I
Clinical Trial, phase II
Clinical Trial, phase III
Clinical Trial, phase IV
Historical Article (for articles about past events)
Biography
Interview
Classical Article
Festschrift
Interview
Journal Article (excludes letter, editorial, news,
etc.
Lectures
Legal Cases
Legislation
Letter
Meta-Analysis (quantitative summary combining
results of independent studies)
Controlled Clinical Trial
Multicenter Study
Randomized Controlled Trial
Comment (for comment on previously published article)
Congresses
Overall (collection of articles)
Consensus Development Conference
Consensus Development Conference, NIH
Controlled Clinical Trial
Corrected and Republished Article
Multicenter Study
News (for medical or scientific news)
Newspaper Article
Overall (collection of articles)
Patient Education Handout
Periodical Index (for cumulated indexes to journals)
Practice Guideline (for specific health care guidelines)
Published Erratum
Randomized Controlled Trial
Retraction of Publication (author’s statement of
retraction)
Dictionary
Retracted Publication (article later retracted by
author)
Directory
Duplicate Publication
Review (includes all types)
Review, Multicase (contains epidemiological
applications)
Editorial
Evaluation Studies
Festschrift
Government Publications
Review of Reported Cases
Review, Tutorial
Guideline (for administrative, procedural guidelines in
Consensus Development Conference
Consensus Development Conference,
NIH
Scientific Integrity Review (US Office of Scientific
general)
Integrity reports)
Practice Guideline (for specific health care
Technical Report
guidelines)
Twin Study
Validation Study
Available by searching the PubMed Help manual for Publication Types; in the Appendices, Table 6; or go directly to:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.table.pubmedhelp.T41
For definitions of terms, visit
http://www.nlm.nih.gov/mesh/pubtypes2006.html
National Library of Medicine Resources
Updated: 7/17/06
Search Field Descriptions and Tags
MEDLINE®/PubMed® Data Element (Field) Descriptions
(Including MeSH® descriptors)
[1AU]
First Author Name
[AB]
[AD]
[AID]
[ALL]
[AU]
[CI]
[CIN]
Abstract
Affiliation
Article Identifier
All Fields
Author
Copyright Information
Comment In
[CN]
[CON]
[CRF]
[CRI]
[DA]
[DCOM]
[DEP]
[DP]
[EDAT]
[EFR]
[EIN]
[EPUB]
[FAU]
[FILTER]
[FIR]
[FPS]
Corporate Author
Comment On
Corrected and republished from
Corrected and republished in
Date Created
Date Completed
Date of Electronic Publication
Publication Date
Entrez Date
Erratum For
Erratum In
Electronic Publication Date
Full Author Name
Filter
Full Investigator
Full Personal Name as Subject
[GN]
[GR]
[GS]
[IP]
[IR]
[IRAD]
[IS]
[JID]
[JT]
[LA]
[LASTAU]
[LR]
[MAJR]
[MH]
[MHDA]
[NM]
[OAB]
[OCI]
[OID]
General Note
Grant Number
Gene Symbol
Issue
Investigator
Investigator Affiliation
ISSN
NLM Unique ID
Full Journal Title
Language
Last Author Name
Last Revision Date
MeSH Major Topic
MeSH Terms
MeSH Date
Substance Name
Other Abstract
Other Copyright Information
Other ID
[ORI]
Original Report In
National Library of Medicine Resources
The first personal author name in a citation.
English language abstract taken directly from published
article
Institutional affiliation and address of the first author
Article ID values supplied by the publisher
Includes all searchable PubMed fields
Authors
Copyright statement provided by the publisher
Reference containing a comment about the article
Corporate author/group names with authorship
responsibility
Reference upon which the article comments
Final, correct version of an article
Original article that was republished in corrected form
Used for internal processing at NLM
Used for internal processing at NLM
Electronic publication date
The date the article was published
The date the citation was added to PubMed
Cites the original article needing the correction
Reference containing a published erratum to the article
See DEP
Full Author Names
Technical tags used by LinkOut (see also subsets)
Full investigator name
Full Personal Name of the subject of the article
Supplemental/descriptive information related to the
document
Research grant numbers and/or contract numbers
Abbreviated gene names (used 1991 through 1996)
Number of the issue, part, or supplement of journal
NASA-funded principal investigator
Affiliation of NASA-funded principal investigator
International Standard Serial Number of the journal
Unique journal ID in NLM's catalog
Full journal title from NLM’s cataloging data
The language in which the article was published
The last personal author name in a citation.
The date a change was made to the record
One of the main topics discussed in the article
NLM's MeSH controlled vocabulary
The date MeSH terms were added to the citation.
Name of a chemical discussed in the article
Abstract supplied by an NLM collaborating organization
Copyright owner
Identification numbers provided by publishers
Cites the original article associated with the patient
summary
Updated: 7/17/06
[OT]
[OTO]
[OWN]
[PA]
[PG]
[PHST]
[PL]
[PMID]
[PS]
[PST]
[PT]
[PUBM]
[RF]
[RIN]
[RN]
[ROF]
[RPF]
[RPI]
[SB]
Other Term
Other Term Owner
Owner
Pharmocologic Action MeSH
Term
Pagination
Publication History Status Date
Place of Publication
PubMed Unique Identifier
Personal Name as Subject
Publication Status
Publication Type
Publishing Model
Number of References
Retraction In
EC/RN Number
Retraction Of
Republished From
Republished In
Subset
[SFM]
Space Flight Mission
[SH]
[SI]
[SO]
[SPIN]
[STAT]
[TA]
[TI]
MeSH Subheading
Secondary Source Identifier
Source
Summary For Patients In
Status Tag
Journal Title Abbreviation
Title
[TIAB]
[TT]
[TW]
[UIN]
[UOF]
[VI]
Title/Abstract
Transliterated Title
Text Word
Update In
Update Of
Volume
Non-MeSH subject terms (keywords)
Organization that provided the Other Term data
Organization acronym that supplied citation data
Substances known to have a particular pharmacologic
action
The full pagination of the article
Publisher supplied dates r
Journal's country of publication
Unique number assigned to each PubMed citation
Individual is the subject of the article
Publication status
The type of material the article represents
Article’s model of print or electronic publishing
Number of bibliographic references for Review articles
Retraction of the article
Enzyme Commission or CAS Registry Number
Article being retracted
Cited article republished or reprinted from another source
Cited article also appears in another source
Sepcificed subset values
NASA-supplied data space flight/mission name and/or
number
To describe more completely a particular aspect of a
subject
Secondary source databanks and accession numbers
Composite field containing bibliographic information
Cites a patient summary article
Used for internal processing at NLM
Standard journal title abbreviation
The title of the article
Words and numbers included in the title abstract of a
citation
Title of the article in the published non-English language
Identified as text by PubMed
Update to the article
The article being updated
Volume number of the journal
For additional information, search the PubMed Help manual for Field Tags
This information combines: Appendices: Box 1. Search Field Descriptions and Tags
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.box.pubmedhelp.Box_1_Search_Field_D
and Appendices: Table 8. MEDLINE Display
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.table.pubmedhelp.T43
National Library of Medicine Resources
Updated: 7/17/06
PubMed®
Stop Words (ignored by PubMed)
a
about
again
all
almost
also
although
always
among
an
and
another
any
are
as
at
be
because
been
before
being
between
both
but
by
can
could
did
do
does
done
due
during
each
either
enough
especially
etc
for
found
from
further
had
has
have
having
here
how
however
i
if
in
into
is
it
its
itself
just
kg
km
made
mainly
make
may
mg
might
ml
mm
most
mostly
must
nearly
neither
no
nor
obtained
of
often
on
our
overall
perhaps
quite
rather
really
regarding
seem
seen
several
should
show
showed
shown
shows
significantly
since
so
some
such
than
that
the
their
theirs
them
then
there
therefore
these
they
this
those
through
thus
to
upon
use
used
using
various
very
was
we
were
what
when
which
while
with
within
without
would
Available by searching the PubMed Help manual for Stop Words; in the Appendices, Table 7;
or go directly to:
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=helppubmed.table.pubmedhelp.T42
National Library of Medicine Resources
Updated: 7/17/06