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PubMed Overview PubMed is a Web-based
retrieval system developed by the National Center
for Biotechnology Information (NCBI) at the
National Library of Medicine. It is part of
NCBI's vast retrieval system, known as Entrez.
PubMed is a database of bibliographic
information drawn primarily from the life
sciences literature. PubMed contains links
to full-text articles at participating
publishers' Web sites as well as links to other
third party sites such as libraries and
sequencing centers. PubMed provides access
and links to the integrated molecular biology
databases maintained by NCBI. The diagram
illustrates the relationships between some of the
information resources in Entrez.
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How Citations are Processed in PubMed Publisher
Supplied Citations Some PubMed citations
are transmitted electronically to PubMed directly
by publishers. This accelerated method of
entering citations means that you have access to
published articles very quickly. These
citations have a PubMed Unique Identifier (PMID)
and the status tag PubMed - as supplied by
publisher.
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In Process PubMed In Process records
provide basic citation information and abstracts
while these records are reviewed for accuracy of
the bibliographic data and assigned subject
headings if the subject of the article is within
the scope of MEDLINE. New records are
generally added Tuesday through Saturday. In
Process records carry the status tag PubMed - in
process. Each In Process record has a
PMID. After MeSH terms, publication types,
and other indexing data are added, the citations
graduate to MEDLINE records.
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MEDLINE MEDLINE is NLM's premier
bibliographic database covering the fields of
medicine, nursing, dentistry, veterinary
medicine, the health care system, the preclinical
sciences, and some other areas of the life
sciences. MEDLINE contains bibliographic
citations and author abstracts from over 4,800
journals published in the United States and in 70
foreign countries. MEDLINE has over 13 million
records from 1966 to the present. Coverage
is worldwide but most records are from English
language sources or have English language
abstracts. MEDLINE contains citations, not
full-text articles (PubMed provides links to some
full-text). Each MEDLINE record is
identified with a PMID and the status tag PubMed
- indexed for MEDLINE. MEDLINE records are
generally added Tuesday through Saturday.
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OLDMEDLINE Citations These citations are
to articles from international biomedical
journals covering the fields of medicine,
preclinical sciences, and allied health
sciences. The over 1.7 million OLDMEDLINE
citations, which do not include abstracts, were
originally printed in hardcopy indexes published
from 1950 through 1965. OLDMEDLINE
citations have been created using standards that
are different from the data entry standards for
MEDLINE records. There are also variations among
OLDMEDLINE citations in the data fields present
as well as in their format, depending on the
original source from which the citations were
obtained. OLDMEDLINE citations lack the
accumulated changes and improvements that have
been made to data in MEDLINE during annual
maintenance. OLDMEDLINE records carry the
status tag PubMed - OLDMEDLINE for Pre1966
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Non-MeSH Indexed Citations Some of the
citations received electronically from publishers
may never become MEDLINE citations. These
records are not assigned MeSH terms because they
do not go through the indexing process.
These records may have either the status tag
PubMed or PubMed - as supplied by publisher
and remain in PubMed even though they are not
MEDLINE citations. There are three sources
of these types of records
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1. Out-of-scope Articles from selectively
indexed MEDLINE journals This may occur
when a particular article in a selectively
indexed journal is out-of-scope for MEDLINE (such
as a geology article in a general scientific
jounal like Science or Nature). These
citations have been reviewed for accurate
bibliographic data. The status tag PubMed
appears on these citations.
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2. Articles from issues of journals published
prior to selection for MEDLINE indexing
These earlier citations will not be indexed with
MeSH headings. Prior to late 2003
o the citations were not reviewed for acurate
bibliographic data o the status tag of
PubMed - as supplied by publisher appears
Beginning in late 2003 o the citations
have been reviewed for accurate bibliographic
data o the status tag of PubMed
appears Example NLM began indexing the
journal Molecular Diagnosis, with v. 4, no. 1,
1999. However, the publisher electronically
supplied NLM with citations from earlier volumes.
The citations from back volumes were entered into
PubMed but will not be indexed with MeSH.
Note Indexing information for a particular
journal can be found in the Indexed In field in
the NLM Catalog. Use PubMeds Journals Database
to link to this information.
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3. Articles archived in PubMed Central from non-
MEDLINE journals. Note Please see the Citation
Status Summary table at http//www.nlm.nih.gov/bsd
/pm_cit_status.html.
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An Introduction to MeSH Vocabulary. What is
MeSH? MeSH is the acronym for "Medical Subject
Headings." MeSH is the authority list of the
vocabulary terms used for subject analysis of
biomedical literature at NLM. MeSH vocabulary is
used for indexing journal articles for MEDLINE
and is also used for cataloging books and
audiovisuals. The MeSH controlled vocabulary is a
distinctive feature of MEDLINE. It imposes
uniformity and consistency to the indexing of
biomedical literature. MeSH terms are arranged in
a hierarchical categorized manner called MeSH
Tree Structures and are updated annually.
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The MeSH Hierarchy This example displays part of
the hierarchy that includes the term, Face.
Notice the narrower terms indented under the
broader terms. When PubMed searches a MeSH term,
it will automatically include narrower terms in
the search, if applicable. This is also called
"automatic explosion."
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Indexing with MeSH Vocabulary NLM indexers
examine articles and assign the most specific
MeSH heading(s) that appropriately describes the
concept(s) discussed. As many as 15
headings may be assigned. When there is no
specific heading for a concept, the indexer will
use the closest, general heading
available. Indexers can also assign Subheadings
to further describe a particular aspect of a MeSH
concept. Examples of Subheadings are
diagnosis, surgery, metabolism, pathology. In
addition to assigning MeSH terms that describe
the topic of the article, the indexer provides
terms that reflect the age group of the
population studied the nature of the
studies e.g., human vs. animal, male vs. female
the material represented (Publication Types)
e.g., Clinical Trials, Editorial, Review In a
later section of this tutorial, you will learn
how to use PubMed's MeSH Database to find MeSH
terms for searching.
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Using PubMed In this module, you will learn how
to use PubMed to conduct a search. By the end of
this module, you should be able to
Navigate PubMed's home page. Use the
sidebar to access PubMed services and resources.
Enter queries to search. Understand
and use Boolean operators. Understand how
PubMed optimizes your search strategy. At the
end of this module, you will have an opportunity
to test your understanding of what has been
presented.
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An Introduction to PubMed's Home Page PubMed's
home page displays the page header
a black bar that provides access to other Entrez
databases a query box where you enter your
search terms feature tabs with access to
additional search features a sidebar with
links to PubMed's Help, other PubMed Services and
related resources the footnote

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The Sidebar Entrez PubMed Text Version links to
the text version of PubMed. Overview provides a
description of PubMed. Help links to detailed
descriptions of all the features, and search and
retrieval options within PubMed. Select FAQ for
answers to frequently asked questions. New/Notew
orthy provides information about recent and
future PubMed system enhancements. E-Utilities
provides information about tools that provide
access to Entrez data outside of the regular web
query interface.
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PubMed Services The Journals Database
allows you to search for journals. The MeSH
Database allows you to browse the MeSH
Vocabulary. The Single Citation Matcher
helps you find citations. Clinical Queries
has built-in search "filters" designed for
clinicians including clinical study category,
systematic reviews, and medical genetics
searches. LinkOut provides users with links
from PubMed and other Entrez databases to a wide
variety of relevant web-accessible online
resources including full-text publications. The
information from this link is intended for groups
who want to provide links that PubMed searchers
may be interested in using. My NCBI
allows you to save search strategies to get
updates, including automatic e-mail updates and
to select filters to group your retrieval by
topics of interest to you.
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• The Sidebar (continued) Related
  Resources
• Order Documents links to information about NLM's
  document ordering feature called Loansome Doc.
• NLM Gateway allows users to search several NLM
  retrieval systems simultaneously.
• TOXNET links to the NLM's TOXNET Web site which
  provides access to a cluster of databases on
  toxicology, hazardous chemicals, and related
  areas.
• Consumer Health links to MedlinePlus, the NLM's
  Web site for consumer health information.
• Clinical Alerts expedite the release of findings
  from the NIH-funded clinical trials where such
  release could significantly affect morbidity and
  mortality.
• ClinicalTrials.gov links to the NIH/NLM Web site
  for current information about clinical research
  studies.
• PubMed Central links to the NIH's digital archive
  of life sciences journal literature. Access to
  this literature is free and unrestricted.

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How It Works To search PubMed, you can simply
enter search terms in the query box. The
Features Tabs directly beneath the query box
provide additional search options -- Limits and
Preview/Index. The other options, History,
Clipboard, and Details, can be used after you
have run your search. The Features Tabs are
covered in greater detail elsewhere in this
course. Regardless of the page you are on,
PubMed, Limits, History, or any of the others --
the query box will always be available to you.
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• Automatic Term Mapping
• Any combination of search terms can be typed in
  the query box. Click the Go button to launch the
  search.
• What is searched?
• PubMed uses an Automatic Term Mapping feature to
  search for unqualified terms. When you click Go,
  PubMed will look for a match in up to four lists.
  
• It looks first for a match in the MeSH
  Translation Table.
• If it doesn't find a match, it looks in the
  Journals Translation Table
• finally in the Author Index.
• As soon as PubMed finds a match, the mapping
  stops.
• That is, if a term matches in the MeSH
  Translation Table, PubMed does not continue
  looking in the next table.

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Automatic Term Mapping (continued) The MeSH
Translation Table contains MeSH Headings
Subheadings Publication Types Entry Term
mappings (also known as synonyms) for MeSH
terms Mappings derived from the Unified Medical
Language System (UMLS) Supplementary Concepts
and synonyms to the Supplementary Concepts 1. If
the term renal transplant is searched, PubMed
will find a match for this in the MeSH
Translation table. 2. Renal transplant is a
synonym for the MeSH term, Kidney
Transplantation. 3. PubMed will search using the
MeSH term as well as the term originally entered.
In addition, the "mapped to" MeSH term will also
be searched in the title and abstract fields in
citations that have yet been assigned MeSH terms.
PubMed automatically searches the MeSH headings
as well as the more specific terms underneath
that heading (if there are any) in the MeSH
hierarchy. This is referred to as exploding the
term.
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Toujours visualiser comment Entrez reformule
votre requête
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cardiac surgery after renal transplant
(("thoracic surgery"TIAB NOT MedlineSB) OR
"thoracic surgery"MeSH Terms OR cardiac
surgeryText Word)
AND afterAll Fields

AND (("kidney transplantation"TIAB NOT
MedlineSB) OR "kidney transplantation"MeSH
Terms OR renal transplantText Word)
???????
10 resultats
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(("thoracic surgery"TIAB NOT MedlineSB) OR
"thoracic surgery"MeSH Terms OR cardiac
surgeryText Word) AND (("kidney
transplantation"TIAB NOT MedlineSB) OR
"kidney transplantation"MeSH Terms OR renal
transplantText Word)
20 résultats
The results of cardiac surgery in 7 patients with
functioning renal transplants are reported. In
all cases surgery was carried out using standard
operative techniques whilst renal perfusion was
enhanced where necessary by the use of a dopamine
infusion. The immediate postoperative course was
uneventful in all cases, though 2 out of 4
patients with ischemic heart disease have since
experienced recurrent symptoms. Cardiac surgery
may be performed in patients with functioning
renal transplants with acceptable mortality and
morbidity.
(("thoracic surgery"TIAB NOT MedlineSB) OR
"thoracic surgery"MeSH Terms OR cardiac
surgeryText Word) AND (("kidney
transplantation"TIAB NOT MedlineSB) OR
"kidney transplantation"MeSH Terms OR renal
transplantText Word OR renal transplantationTex
t Word OR "kidney transplant"Text Word)
25 résultats
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Automatic Term Mapping (continued) The Journals
Translation Table contains Full journal titles
MEDLINE title abbreviations International
Standard Serial Numbers (ISSN) If you searched
for the journal of cell biology, for example,
PubMed would translate this as "J Cell
Biol"Journal. What if a journal name is also
a MeSH heading -- Cell, for example? PubMed will
first check in the MeSH Translation Table, find a
match and stop the mapping process. The search
will not include the term as a journal name, so
the unqualified search for cell will not include
a search for citations from the journal,
Cell. Searching for journal titles will be
covered in a later module of this
course. Finally, PubMed will look in the Author
Index if it cannot find a match in the
translation tables and if the word has one or two
letters after it.
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Automatic Term Mapping (continued) If no match
is found? There will be times when PubMed is
unable to match a search term with either of the
translation tables or the Author Index. PubMed
will then search the individual words in All
Fields. Individual terms will be combined (ANDed)
together. In the illustration, the search
criteria pressure point is translated by PubMed.
Pressure matched in the MeSH Translation Table,
but point did not match in any of the tables, and
it is, therefore, searched in All Fields.
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Automatic Term Mapping (continued) Summary In
summary, then, let's see how PubMed searches for
the search query head lice shampoo. PubMed will
then combine the results (with AND) to produce a
single search strategy (i.e., (("pediculus"TIAB
NOT MedlineSB) OR "pediculus"MeSH Terms OR
head liceText Word) AND shampooAll Fields ).
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Phrase Searching PubMed searches for phrases
under these conditions The phrase is entered
with a search tag kidney allograft tw The
phrase is enclosed in double quotes. (The absence
of a search tag indicates the search should be
conducted in All Fields.) "kidney
allograft" The term is hyphenated first-line
The term is truncated kidney allograft Example
"pressure point"
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Phrase Searching (continued) These formats for
phrase searching instruct PubMed to bypass
automatic term mapping. Instead PubMed looks for
the phrase in its Index of searchable terms. If
the phrase is in the Index, PubMed will retrieve
citations that contain the phrase. PubMed may
fail to find a phrase because it is not in the
Index. Your phrase may actually appear in
citation and abstract data, but may not be in the
Index. If this is the case, the double quotes are
ignored and the phrase is processed using
Automatic Term Mapping. Note Using quotes
bypasses Automatic Term Mapping, which may be
beneficial to your search. Therefore, try your
search with and without quotes and compare your
results.
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Author Searching The format for author searching
is last name plus initials. PubMed will
automatically truncate the author's name to
account for varying initials. To turn off
automatic truncation of an author's name,
surround the name with double quotes and use the
au tag. If you are searching with last name
only, be sure to use the au tag.
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Truncation Truncation can be used when you want
PubMed to find all terms that begin with a given
text string. Truncation is represented by the
asterisk (), sometimes referred to as a
"wildcard." For example, let's say you are trying
to search all terms that have the root, mimic. If
you search mimic PubMed will retrieve words such
as mimic, mimics, mimicing, etc. PubMed has no
single character truncation symbol. Truncation
Tips PubMed restricts retrieval to the first
600 variations of the truncated term. When this
occurs, PubMed will display a warning message.
Truncation turns off automatic term mapping
and the automatic explosion of MeSH terms. For
example, heart attack will not map to the MeSH
term Myocardial Infarction or include any of the
more specific indentions, such as Myocardial
Stunning.
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Spell Check Feature Spell check suggests
alternative spellings for search terms that
include misspellings. Results from a search will
display along with an option to link to the
alternative spelling to provide users with an
easy way to retrieve results for untagged words
that are misspelled. Terms entered with a
search tag (e.g., mh majr tw) will not
generate alternative spellings. Note The
alternative spellings are not based on a
dictionary but rather the frequency with which a
term appears in PubMed. The spell checking
function will not display an alternative spelling
for misspellings that have a high frequency of
occurrence in PubMed or for terms with numbers or
fewer than 5 characters. The feature works best
for terms with multiple words.
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Stopwords PubMed also refers to a list of
commonly found words that are referred to as
"stopwords." Stopwords are words that, if
indexed, could potentially return every document
in the database if the word was used in a search
statement. Consequently, commonly found words
are not indexed and PubMed will ignore them. Go
to PubMed's Help to view the list of
stopwords. You should now understand how PubMed
takes your query, translates it, and retrieves
citations to articles. In the next topic, we'll
look at developing search strategies. Click Next
when you are ready to continue.
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Developing a Search Strategy Before you can
search for any information, you should first
develop a search strategy. What is a Search
Strategy? A search strategy is a plan that
helps you look for the information you need.
Search Strategy Tips Identify the key concepts.
Determine alternative terms for these concepts,
if needed. Refine your search to dates, study
groups, etc., as appropriate. Practice helps.
Strategies and styles will differ according to
personal choice and professional
discipline. Time now to move on to the next
topic, Boolean logic. Click Next when you are
ready to continue.
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