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| ![](media/image1  | **PubMed Expert Searching:**                     |
| .png){width="1.89 |                                                  |
| 58333333333333in" | **Using PubMed to Get Advanced Results**         |
| height="1.614     |                                                  |
| 5833333333333in"} |                                                  |
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|                   |                                                  |
+-------------------+--------------------------------------------------+

**February 2006**

![](media/image2.png){width="4.75in" height="0.625in"}

**Table of Contents**

[Agenda 2](#agenda)

[Searching with MeSH 3](#searching-with-mesh)

[Basic Information about MeSH: 3](#basic-information-about-mesh)

[MeSH Particulars 4](#mesh-particulars)

[MeSH Tree Structure 8](#mesh-tree-structure)

[MeSH Browsers & Databases 15](#mesh-browsers-databases)

[OLDMEDLINE Citations 18](#oldmedline-citations)

[Automatic term mapping 21](#automatic-term-mapping)

[Searching With Field Tags 25](#searching-with-field-tags)

[Search Rules and Syntax 25](#search-rules-and-syntax)

[Search Field Abbreviations 26](#search-field-abbreviations)

[Subset \[SB\] 38](#subset-sb)

[Filter \[filter\] or \[sb\] 39](#filter-filter-or-sb)

[Discipline Searching 44](#discipline-searching)

[Veterinary Medicine Discipline Searching
46](#veterinary-medicine-discipline-searching)

[Nursing Discipline Searching 48](#nursing-discipline-searching)

[Allied Health Discipline Searching
50](#allied-health-discipline-searching)

[Pharmacologic Action Headings (PA) and Searching for Drug Information
53](#pharmacologic-action-headings-pa-and-searching-for-drug-information)

[Pharmacological Actions \[PA\] 56](#pharmacological-actions-pa)

[My NCBI 59](#my-ncbi)

[Setting up a My NCBI account: 59](#setting-up-a-my-ncbi-account)

[Setting Filters in My NCBI 61](#setting-filters-in-my-ncbi)

[LinkOut for Libraries and My NCBI
64](#linkout-for-libraries-and-my-ncbi)

[Preferences in My NCBI 69](#preferences-in-my-ncbi)

[LinkOut 69](#linkout)

[Searching with Clinical Queries 71](#searching-with-clinical-queries)

[Clinical Queries 71](#clinical-queries)

[Systematic Reviews 73](#systematic-reviews)

[Medical Genetics Searches 74](#__RefHeading___Toc119233570)

[Creating Web Links to PubMed 75](#creating-web-links-to-pubmed)

[Searching 76](#searching)

[Formats 77](#formats)

[Date Ranges 77](#date-ranges)

[Relative Dates 78](#relative-dates)

# Agenda

Welcome, introductions, review of handouts 15 minutes What do you hope
to learn from this class?

What skills do you feel you need in order to become an expert searcher?

MeSH 60 minutes

Break 15 minutes

Field Tags and LinkOut 30 minutes

Search Exercises with Field Tags 20 minutes

Break 15 minutes

Searching in Specific Disciplines 15 minutes

My NCBI 20 minutes

Clinical & Special Queries 20 minutes

Additional Tips and Tricks: Building Web Links 15 minutes

Wrap up and Evaluations 15 minutes

# Searching with MeSH

## Basic Information about MeSH:

-   MeSH is an acronym for [Me]{.underline}dical [S]{.underline}ubject
    [H]{.underline}eadings. It is the controlled vocabulary used to
    index articles in MEDLINE and *Index Medicus* and it is used for
    cataloging books and audiovisuals.

-   The home page for the MeSH section of NLM is located at
    <http://www.nlm.nih.gov/mesh/meshhome.html>

-   MeSH is revised annually. The *NLM Technical Bulletin* will identify
    when the revision has been completed each year and the significant
    changes that were made. Access the *Technical Bulletin* at
    <http://www.nlm.nih.gov/pubs/techbull/tb.html>

-   Indexers typically assign 10-15 MeSH terms to a journal article with
    major topics indicated with an asterisk (\*). Indexers use the most
    specific MeSH term available. Searchers should, too.

    -   Note: In *indexing*, the \* denotes the MeSH Major Heading. In
        the Citation display format in PubMed, the MeSH terms assigned
        to that citation will be displayed and the \* denotes the MeSH
        Major Heading(s).

    -   In *searching*, PubMed interprets an asterisk (\*) as a
        truncation symbol. The asterisk (\*) should be used very
        carefully in searching PubMed as it turns off the Automatic Term
        Mapping function.

**What is a controlled vocabulary?**

-   A controlled vocabulary is a list of words approved for indexing.
    Only these words are allowed as indexing terms.

**Why use a controlled vocabulary?**

-   A controlled vocabulary provides uniformity and consistency to
    indexing.

```{=html}
<!-- -->
```
-   Indexing with a controlled vocabulary allows for retrieval of all
    relevant information with the use of a single, key term.

-   In key word searching, searchers have to know all possible spelling
    variations (color and colour, for example) and all possible terms
    related to the subject matter (dog, canine, doggy, pooch, puppie,
    pup, Fido, etc.) in order to find the needed information. A
    controlled vocabulary eliminates this and makes searching more
    efficient.

## MeSH Particulars

-   There are four major components of the MeSH vocabulary:

    -   [Descriptors]{.underline} (also known as Main Headings or MeSH
        Headings)

        -   Descriptors describe concepts.

        -   These are generally nouns.

        -   These are generally NOT brand names or personal names.

        -   Examples of descriptors:

> Seasonal Affective Disorder
>
> Brain
>
> Mentors
>
> Liver Diseases
>
> New South Wales
>
> Hair Follicle

-   When articles are indexed for Medline, indexing is to the most
    specific term available. To accomplish this specificity, descriptors
    are often combined with subheadings.

```{=html}
<!-- -->
```
-   [Subheadings]{.underline} (also known as Qualifiers)

    -   These are generally adjectives that describe the nouns
        (descriptors).

    -   Subheadings add specificity. They answer the question: "What
        aspect of this main heading is the author writing about or
        discussing?"

    -   Examples of subheadings:

> Diet therapy
>
> Adverse effects
>
> Prevention and control
>
> Economics

-   Think of using a subheading whenever there is an "of" in a research
    question.

> What is the mortality rate of asthma?
>
> Asthma = descriptor
>
> Mortality = subheading
>
> What are the causes of hypercholesterolemia?
>
> Hypercholesterolemia = descriptor
>
> Etiology = subheading
>
> What are the adverse side effects of tamoxifen?
>
> Tamoxifen = descriptor
>
> Adverse effects = subheading

-   A list of subheadings and the two letter abbreviation associated
    with each is at the end of this section.

```{=html}
<!-- -->
```
-   [Supplementary Concept Records]{.underline}

    -   These are generally chemical and substance names.

    -   There are over 130,000 Supplementary Concepts included in MeSH.

    -   These are updated daily.

    -   Examples:

> Tonicaine
>
> Benorilate
>
> Atavorstatin
>
> Chromium Sulfate

-   A sample supplementary concept record:

![](media/image3.png){width="3.7805555555555554in"
height="4.186805555555556in"}

**Record Type** = C for Supplemental Concepts

**Registry Number** = Unique number assigned to chemicals by the
Chemical Abstracting Service or a code for enzymes assigned by the
Commission on Biological Nomenclature

**Heading mapped to** = Descriptor used for indexing this substance in
MEDLINE

**Previous Indexing** = MeSH terms used before the current Descriptor
was available; also, terms removed from the Heading Mapped to field over
time

**Source** = Citations to articles in which the chemical has been
identified

**Thesaurus ID** = Authoritative reference where the chemical is listed

**Pharmacologic Action** = Action of a drug or chemical as reported in
the literature

**Frequency** = Number of times the chemical has been identified in
MEDLINE journals

**Date of Entry** = Date record was added to the system

Other available fields in Supplemental Concept Records:

**CAS Type 1 Name** = Systematic name of a chemical which defines its
structure

**Related Number** = Registry numbers for salts and/or stereoisomers

**Indexing Information** = Other MeSH terms that an indexer should
consider using

**Note** = Additional information

-   [Publication Types]{.underline}

    -   These are terms that describe publication types.

```{=html}
<!-- -->
```
-   All available publication types may be viewed by using the
    "Preview/Index" function of PubMed. Access the Preview/Index page,
    select "Publication Type" from the All Fields drop down menu and
    then click on Index:

> ![](media/image4.png){width="5.374305555555556in" height="2.4375in"}
>
> A listing of all the available publication types and their scope notes
> may also be found at <http://www.nlm.nih.gov/mesh/pubtypes2005.html>
>
> A listing is also found at the end of this section.

-   Additional components of the MeSH vocabulary: In addition to
    descriptors (MeSH main headings), subheadings (qualifiers),
    supplementary concepts, and publication types, there are two
    additional vocabulary groups in MeSH:

    -   [CAS Registry Number/EC Number]{.underline}

        -   This is a unique 5 -- 9 digit number in hyphenated format
            representing the Chemical Abstracts number. The Chemical
            Abstracts number is sometimes referred to as the RN number.

> Examples:
>
> 439-14-5 is the CAS registry number for diazepam (Valium)
>
> 54910-89-3 is the registry number for fluoxetine (Prozac)

-   The EC numbers are classification numbers for enzymes. Each begins
    with "EC" and is followed by four numbers separated by periods.

> Examples:
>
> EC 1.1.3.4 is the EC number for glucose oxidase.
>
> EC 4.1.99.1 is the EC number for tryptophanase.

-   An RN or EC number may be used to search PubMed.

```{=html}
<!-- -->
```
-   The registry numbers for substances may be seen in the "Medline"
    type display for a citation in PubMed (the RN field) or in the MeSH
    section's browser in appropriate records.

    -   [Age Groups]{.underline}

-   These are MeSH headings that indicate the age of human subjects
    discussed in an article.

-   Age Groups are found in the "Persons" tree of the MeSH hierarchy

![](media/image5.png){width="2.988888888888889in"
height="2.1041666666666665in"}

## MeSH Tree Structure

-   Descriptors are arranged in a hierarchy known as the Tree Structure.

-   There are 16 main branches to the MeSH Tree. These are the broadest
    categorizations in MeSH and narrower, more specific terms reside
    under each of these (the branches). The trees are:

> A. Anatomy
>
> B. Organisms
>
> C. Diseases
>
> D. Chemicals and Drugs
>
> E. Analytical, Diagnostic and Therapeutic Techniques and Equipment
>
> F. Psychiatry and Psychology
>
> G. Biological Sciences
>
> H. Physical Sciences
>
> I. Anthropology, Education, Sociology and Social Phenomena
>
> J. Technology and Food and Beverages
>
> K. Humanities
>
> L. Information Science
>
> M. Persons
>
> N. Health Care
>
> V. Publication Characteristics
>
> Z. Geographic Locations

-   Descriptors can "live" on more than one branch of the MeSH Tree.

> Ear is part of the Body Regions tree (A01)
>
> Ear is also part of the Sense Organs tree (A09)

-   See <http://www.nlm.nih.gov/mesh/MBrowser.html> for an interactive
    link to the Tree Structure. Click on the "Navigate from Tree Top"
    button. This will allow exploration of any tree from top (broadest
    concepts) to bottom (most specific concepts).

-   MeSH descriptors are also assigned numbers. Note, however, that MeSH
    numbers are [not]{.underline} used for searching. They simply
    indicate the relationships between concepts. There is a direct
    relationship between the length of the number and the specificity of
    the term. For example:

> Asthma \-\-\-\-\-\-\-\-\-\-\-\-\-\-- \[C08.127.108\] is more specific
> than
>
> Bronchial Diseases \-- \[C08.127\]
>
> New England \-\-\-\-\-\-\-- \[Z01.107.567.875.550\] is more specific
> than
>
> United States \-\-\-\-\-\-\-\-- \[Z01.107.567.875\]

**Exploding**

-   The hierarchical arrangement of MeSH allows for exploding. Exploding
    refers to the automatic inclusion of the more specific MeSH terms in
    a search when a broad MeSH term is chosen for a search.

> For a simple example, the MeSH term SMOKING looks like this in the
> tree structure:
>
> ![](media/image6.png){width="4.334027777777778in"
> height="1.7083333333333333in"}
>
> A PubMed search using the MeSH term SMOKING will automatically explode
> -- meaning that it will also include the more specific MeSH term
> MARIJUANA SMOKING in the search.
>
> The MeSH tree for other terms can be quite a bit longer and more
> complex meaning that exploding those terms includes *many* narrower
> terms. See the MeSH term WOUNDS AND INJURIES for a good example.

-   The automatic exploding of MeSH descriptors can be turned off using
    the "Do not explode" option in the Entrez MeSH database's full
    display:

![](media/image7.png){width="5.460416666666666in"
height="3.0180555555555557in"}

-   Or, the automatic exploding of MeSH descriptors may be turned off by
    using the \[MESH:NOEXP\] tag in the search:

> ![](media/image8.png){width="5.134722222222222in"
> height="1.2083333333333333in"}

-   Qualifiers (subheadings) are also subject to automatic exploding. A
    list of the families of qualifiers appears at the end of this
    section. To turn off the automatic exploding feature, use the
    \[sh:noexp\] tag for floating subheadings and the \[mh:noexp\] tag
    for MeSH heading/subheading combinations.

**Using Qualifiers (subheadings)**

-   When articles are indexed for Medline, the MeSH terms are often (not
    always) accompanied by a subheading because, as noted above,
    indexers index to the most specific term available.

```{=html}
<!-- -->
```
-   Subheadings are attached to MeSH headings in the following manner:
    MeSH**/**Subheading (or MH/sh). The subheadings may be spelled out
    in full or the official two letter abbreviation may be used.

> For example:
>
> What are the adverse side effects of tamoxifen?
>
> Use: Tamoxifen/adverse effects
>
> Tamoxifen/ae
>
> What is the cause of hypercholesterolemia?
>
> Use: Hypercholesterolemia/etiology
>
> Hypercholesterolemia/et

-   Only one subheading may be attached to a MeSH heading at a time. It
    is not proper to use MH/sh/sh.

-   To include several subheadings in a search:

    1.  Use the PubMed MeSH Database and select the desired subheadings
        from the full display screen. Then, choose an option from the
        "Send to" drop-down box to add the headings/subheadings to the
        search box.

    2.  "OR" together the MH/sh combinations in the PubMed search box.
        For example: asthma/mortality OR asthma/etiology OR
        asthma/therapy

-   Floating subheadings refers to the practice of using a subheading in
    a search *without* attaching it to a particular MeSH descriptor.
    This involves combining a MeSH heading with a subheading using the
    Boolean AND.

-   The decision to "free-float" a subheading is typically done when the
    subheading of interest is one that cannot be applied to the MeSH
    descriptor being searched:

> Childrearing \[mh\] AND complications \[sh\]

-   Using floating subheadings may result in a lot of noise (false drops
    or false hits) in the search results.

> Note: These searches are NOT identical:
>
> urticaria/im
>
> urticaria\[mh\] AND immunology\[sh\]
>
> urticaria AND immunology
>
> urticaria/im\[mh:noexp\]

-   The search "urticaria\[mh\] AND immunology\[sh\]" will result in
    citations indexed as urticaria/immunology, but it will also pull up
    urticaria/chemically induced or pneumonia/immunology or any other
    citation in which a MeSH heading is combined with /immunology.

-   The search "urticaria/im" will result in a smaller result set, but a
    more specific one. Remember, however, that both MeSH and the
    subheadings automatically explode to include narrower terms from the
    hierarchy.

-   The most specific search is utricaria/im\[mh:noexp\] as it will
    retrieve only citations that have "urticaria/immunology" in the
    indexing.

```{=html}
<!-- -->
```
-   When using MeSH for searching, remember that the most specific MH or
    MH/sh combination is used to index articles. Searchers need to do
    the same in order to get the most relevant results.

**SUBHEADINGS**

  ------------------------- ------- -------------------------------- ------
  Abnormalities             AB      Isolation & Purification         IP

  Administration & Dosage   AD      Legislation & Jurisprudence      LJ

  Adverse Effects           AE      Manpower                         MA

  Agonists                  AG      Metabolism                       ME

  Analogs & Derivatives     AA      Methods                          MT

  Analysis                  AN      Microbiology                     MI

  Anatomy & Histology       AH      Mortality                        MO

  Antagonists & Inhibitors  AI      Nursing                          NU

  Biosynthesis              BI      Organization & Administration    OG

  Blood                     BL      Parasitology                     PS

  Blood Supply              BS      Pathogenicity                    PY

  Cerebrospinal Fluid       CF      Pathology                        PA

  Chemical Synthesis        CS      Pharmacokinetics                 PK

  Chemically Induced        CI      Pharmacology                     PD

  Chemistry                 CH      Physiology                       PH

  Classification            CL      Physiopathology                  PP

  Complications             CO      Poisoning                        PO

  Congenital                CN      Prevention & Control             PC

  Contraindications         CT      Psychology                       PX

  Cytology                  CY      Radiation Effects                RE

  Deficiency                DF      Radiography                      RA

  Diagnosis                 DI      Radionuclide Imaging             RI

  Diagnostic Use            DU      Radiotherapy                     RT

  Diet Therapy              DH      Rehabilitation                   RH

  Drug Effects              DE      Secondary                        SC

  Drug Therapy              DT      Secretion                        SE

  Economics                 EC      Standards                        ST

  Education                 ED      Statistics & Numerical Data      SN

  Embryology                EM      Supply & Distribution            SD

  Enzymology                EN      Surgery                          SU

  Epidemiology              EP      Therapeutic Use                  TU

  Ethics                    ES      Therapy                          TH

  Ethnology                 EH      Toxicity                         TO

  Etiology                  ET      Transmission                     TM

  Genetics                  GE      Transplantation                  TR

  Growth & Development      GD      Trends                           TD

  History                   HI      Ultrasonography                  US

  Immunology                IM      Ultrastructure                   UL

  Injuries                  IN      Urine                            UR

  Innervation               IR      Utilization                      UT

  Instrumentation           IS      Veterinary                       VE

                                    Virology                         VI
  ------------------------- ------- -------------------------------- ------

**Families of Subheading Explosions**

  --------------------- ------------------------- -----------------------
  **adverse effects**   **etiology**              **physiology**

  poisoning             chemically induced        genetics

  toxicity              complications             growth & development

                        secondary                 immunology

  analysis              congenital                metabolism

  blood                 embryology                biosynthesis

  cerebrospinal fluid   genetics                  blood

  isolation &           immunology                cerebrospinal fluid
  purification                                    

  urine                 microbiology              deficiency

                        virology                  enzymology

  anatomy & histology   parasitology              pharmacokinetics

  blood supply          transmission              urine

  cytology                                        physiopathology

  pathology             metabolism                secretion

  ultrastructure        biosynthesis              

  embryology            blood                     statistics & numer data

  abnormalities         cerebrospinal fluid       epidemiology

  innervation           deficiency                ethnology

                        enzymology                mortality

  chemistry             pharmacokinetics          supply & distribution

  agonists              urine                     utilization

  analogs & derivatives                           

  antagonists &         microbiology              surgery
  inhibitors                                      

  chemical synthesis    virology                  transplantation

                                                  

  complications         organization & admin      therapeutic use

  secondary             economics                 administration & dosage

                        legislation &             adverse effects
                        jurisprudence             

  cytology              manpower                  contraindications

  pathology             standards                 poisoning

  ultrastructure        supply & distribution     

                        trends                    therapy

  diagnosis             utilization               diet therapy

  pathology                                       drug therapy

  radiography           pharmacology              nursing

  radionuclide imaging  administration & dosage   prevention & control

  ultrasonography       adverse effects           radiotherapy

                        poisoning                 rehabilitation

  embryology            toxicity                  surgery

  abnormalities         agonists                  transplantation

                        antagonists & inhibitors  

  **epidemiology**      contraindications         

  ethnology             diagnostic use            

  mortality             pharmacokinetics          
  --------------------- ------------------------- -----------------------

**PubMed Publication Types**

  ----------------------------------- -----------------------------------
  Addresses                           Interview

  Bibliography                        Journal Article (excludes letter,
                                      editorial, news, etc.

  Biography                           Lectures

  Case Reports                        Legal Cases

  Classical Article (for republished  Legislation
  seminal articles)                   

  Clinical Conference (for reports of Letter
  clinical case conferences only)     

  Clinical Trial (includes all types  Meta-Analysis (quantitative summary
  and phases of clinical trials)      combining results of independent
                                      studies)

  Clinical Trial, phase I             Multicenter Study

  Clinical Trial, phase II            News (for medical or scientific
                                      news)

  Clinical Trial, phase III           Newspaper Article

  Clinical Trial, phase IV            Overall (collection of articles)

  Comment (for comment on previously  Patient Education Handout
  published article)                  

  Congresses                          Periodical Index (for cumulated
                                      indexes to journals)

  Consensus Development Conference    Practice Guideline (for specific
                                      health care guidelines)

  Consensus Development Conference,   Published Erratum
  NIH                                 

  Controlled Clinical Trial           Randomized Controlled Trial

  Corrected and Republished Article   Retraction of Publication (author's
                                      statement of retraction

  Dictionary                          Retracted Publication (article
                                      later retracted by author)

  Duplicate Publication               Review (includes all types)

  Editorial                           Review, Multicase (contains
                                      epidemiological applications)

  Evaluation Studies                  Review of Reported Cases

  Festschrift                         Review, Tutorial

  Government Publications             Scientific Integrity Review (US
                                      Office of Scientific Integrity
                                      reports)

  Guideline (for administrative,      Technical Report
  procedural guidelines in general)   

  Historical Article (for articles    Twin Study
  about past events)                  

                                      Validation Study
  ----------------------------------- -----------------------------------

## 

## 

## 

## MeSH Browsers & Databases

-   There are [two]{.underline} MeSH browsers available: the Entrez MeSH
    Database (PubMed) and the MeSH section's online browser.

    -   The Entrez MeSH Database may be accessed via a link on the left
        hand side (blue frame) of the PubMed page.

    -   The MeSH section's browser is located at
        <http://www.nlm.nih.gov/mesh/MBrowser.html>

-   Both of these will identify MeSH terms and show the section of the
    MeSH tree pertinent to that concept. Beyond that, they display much
    of the same information in different ways and they provide different
    functionality. For example, look at the browser information for the
    MeSH term COMMON COLD:

> From the Entrez MeSH Database's full display:

![](media/image9.png){width="6.25in" height="4.238888888888889in"}

-   In the Entrez MeSH Database, a definition of the descriptor is
    provided.

```{=html}
<!-- -->
```
-   Subheadings are presented here with check boxes. Users may select
    none, one, or more subheadings to add to their search.
    [NOTE]{.underline}: In the Entrez MeSH database the subheadings
    listed are those that have been paired at least once with a
    descriptor and *may not reflect current rules* for
    heading/subheading use.

-   Two other search related options are available from this page:

    -   Restrict Search to Major Topic headings only

    -   Do Not Explode this term

-   A PubMed search may be built directly from this Database using the
    "Send to" options at the top of the page \[not pictured here\].

> **From the MeSH section's browser**:

  ---------------- ----------------------------------------------------------------------------------------------------------
  **MeSH Heading** Common Cold

  **Tree Number**  [C02.782.687.207](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi#TreeC02.782.687.207%23TreeC02.782.687.207)

  **Tree Number**  [C08.730.162](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi#TreeC08.730.162%23TreeC08.730.162)

  **Annotation**   often caused by a picornavirus

  **Scope Note**   A catarrhal disorder of the upper respiratory tract, which may be viral, a mixed infection, or an allergic
                   reaction. It is marked by acute coryza, slight rise in temperature, chilly sensations, and general
                   indisposition. (Dorland, 27th ed)

  **Entry Term**   Cold, Common

  **Entry Term**   Coryza, Acute

  **Allowable      [BL](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=BL&field=qual)
  Qualifiers**     [CF](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=CF&field=qual)
                   [CI](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=CI&field=qual)
                   [CL](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=CL&field=qual)
                   [CN](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=CN&field=qual)
                   [CO](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=CO&field=qual)
                   [DH](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=DH&field=qual)
                   [DI](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=DI&field=qual)
                   [DT](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=DT&field=qual)
                   [EC](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=EC&field=qual)
                   [EH](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=EH&field=qual)
                   [EM](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=EM&field=qual)
                   [EN](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=EN&field=qual)
                   [EP](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=EP&field=qual)
                   [ET](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=ET&field=qual)
                   [GE](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=GE&field=qual)
                   [HI](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=HI&field=qual)
                   [IM](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=IM&field=qual)
                   [ME](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=ME&field=qual)
                   [MI](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=MI&field=qual)
                   [MO](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=MO&field=qual)
                   [NU](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=NU&field=qual)
                   [PA](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=PA&field=qual)
                   [PC](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=PC&field=qual)
                   [PP](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=PP&field=qual)
                   [PS](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=PS&field=qual)
                   [PX](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=PX&field=qual)
                   [RA](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=RA&field=qual)
                   [RH](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=RH&field=qual)
                   [RI](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=RI&field=qual)
                   [RT](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=RT&field=qual)
                   [SU](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=SU&field=qual)
                   [TH](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=TH&field=qual)
                   [TM](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=TM&field=qual)
                   [UR](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=UR&field=qual)
                   [US](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=US&field=qual)
                   [VE](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=VE&field=qual)
                   [VI](http://www.nlm.nih.gov/cgi/mesh/2003/MB_cgi?term=VI&field=qual)

  **Unique ID**    D003139
  ---------------- ----------------------------------------------------------------------------------------------------------

-   The Entry terms are synonyms or concepts included by this MeSH
    heading. If an entry term is typed into the search box in PubMed it
    will map to the designated descriptor. In this example, "Coryza,
    Acute" will map directly to the Mesh descriptor COMMON COLD.

-   The annotation presents additional information on the concept that
    may be of use to indexers and/or searchers.

-   The allowable qualifiers are the subheadings (qualifiers) that may
    be used with this term. In the MeSH section browser, these two
    letter abbreviations for each subheading are hyperlinks that, if
    followed, will link directly to the record for the subheading.

> **A Comparison of the two Browsers**:

+-------------------------------+---+-----------------------------------+
| **Entrez MeSH Database**      |   | **NLM MeSH Browser**              |
+-------------------------------+---+-----------------------------------+
|                               |   |                                   |
+-------------------------------+---+-----------------------------------+
| Definition                    |   | Definition (scope note)           |
+-------------------------------+---+-----------------------------------+
| No annotation                 | ↔ | Annotation                        |
+-------------------------------+---+-----------------------------------+
| Entry terms                   |   | Entry terms                       |
+-------------------------------+---+-----------------------------------+
| History: year concept added   |   | History: year concept added to    |
| to MeSH                       |   | MeSH                              |
+-------------------------------+---+-----------------------------------+
| Previous indexing available   |   | Previous indexing available       |
+-------------------------------+---+-----------------------------------+
| "See also" concepts available |   | "See also" concepts available &   |
| & hyperlinked                 |   | hyperlinked                       |
+-------------------------------+---+-----------------------------------+
| RN numbers not searchable     | ↔ | RN numbers searchable             |
+-------------------------------+---+-----------------------------------+
| Subheading records available. |   | Subheading records available.     |
| These must be searched as     |   | Within a Descriptor record, the   |
| separate terms.               |   | available subheadings are         |
|                               |   | hyperlinked. Note: This database  |
| Note: subheadings appear here |   | shows the subheadings that are    |
| which may *not* be allowed    |   | currently allowed for use with a  |
| for use with this particular  |   | given MeSH heading.               |
| heading currently.            |   |                                   |
+-------------------------------+---+-----------------------------------+
| Pharmacological action data   |   | Pharmacological action data       |
| (2003)                        |   | available                         |
+-------------------------------+---+-----------------------------------+
| Can build a PubMed search     | ↔ | Can NOT build a PubMed search     |
| here                          |   | here                              |
+-------------------------------+---+-----------------------------------+
| Provides some help for        | ↔ | Words must be spelled correctly   |
| misspelled words              |   | in order to be searched here      |
+-------------------------------+---+-----------------------------------+
| Suggests other terms of       |   | Provides the option of searching  |
| possible interest             |   | for the exact term, all           |
|                               |   | fragments, or any fragment        |
+-------------------------------+---+-----------------------------------+
| No permuted index available   | ↔ | Permuted index available          |
+-------------------------------+---+-----------------------------------+
| Supplementary concept records |   | Supplementary concept records     |
| available as of 10-14-2004    |   | available                         |
+-------------------------------+---+-----------------------------------+

NOTE: The NLM Gateway also has a database of terms called the Term
Finder. It is available from a link on the Gateway page or directly from
<http://gateway.nlm.nih.gov/gw/Cmd?GMBasicSearch&loc=nccs>

The Term Finder provides some of the same functionality as seen in the
two browsers discussed above as well as additional functionality
(particularly when it comes to non-MeSH terms).

## OLDMEDLINE Citations 

See <http://www.nlm.nih.gov/pubs/techbull/so03/so03_oldmedline.html> for
the entire *NLM Technical Bulletin* article.

On September 30, 2003, over 1.5 million OldMedline citations were added
to PubMed. These citations were originally printed in hardcopy indexes
published from 1953 through 1965.

The data in the OldMedline records differ from that in the current
PubMed records in several important ways:

-   *Abstract*s: OLDMEDLINE citations have no abstracts.

-   *Publication Type*: Only "Journal Article" was used.

-   *Language*: Some citations will indicate "und" because the actual
    foreign language was not specified and is, therefore, undetermined.

-   *Article titles*: Some are all in caps; over 28,000 citations show
    "Not Available" as the title because they lack English translations
    of the titles.

-   *Other Term*: This field contains the original MeSH terms assigned
    at the time the records were first established. NLM has, since late
    2005, been working to add current MeSH headings to these OLDMEDLINE
    citations. See note at end of this section.

Considerations for PubMed searching of OLDMEDLINE citations:

Status Tag: The **\[PubMed - OLDMEDLINE for Pre1966\]** tag identifies
these citations.

Subset: Searches can be limited to OLDMEDLINE using a new subset created
for these citations. You may select, OLDMEDLINE for Pre1966, from the
Subsets menu in Limits. Alternatively, this subset can be used directly
in a search as **oldmedline \[sb\]**.

Other Term field: The Other Term field in PubMed contains non-MeSH
subject terms. In the case of OLDMEDLINE citations, this field contains
the original index terms. These terms are not updated. These terms are
all preceded by an asterisk to indicate a major concept. (Asterisks are
for display only. You cannot search Other Terms with a major concept
tag.) The OT field is searchable with the Text Word \[TW\] and Other
Term \[OT\] search tags.

Entrez Date: The Entrez date for OLDMEDLINE citations is created using
the **date of publication** on the citation. This is necessary to
prevent older citations from displaying near the top of retrieval as the
default display order in PubMed is reverse chronological order of the
Entrez date (i.e., last in - first out).

Journal Title Abbreviations: Journal title abbreviations may have been
changed from the abbreviation found on the original OLDMEDLINE citation;
however, using an old abbreviation will retrieve across all years.
NLM\'s catalog, LOCATORplus will have old title abbreviation data on
serial records for OLDMEDLINE journals. As always, full title names can
be used for searching in PubMed.

Personal Name as subject \[PS\]: Many OLDMEDLINE citations reference
articles about historical figures. If you want to search for an atypical
name, use the following examples as a guide:

> louis xiv \[ps\]
>
> st paul \[ps\]

More typical names can be searched as in this example:

> von gudden b \[ps\]

Searching considerations:

-   OLDMEDLINE citations do not have fields frequently found on MEDLINE
    records, including: Abstract, Affiliation, EC/RN Number and Name of
    Substances \[RN\], Grant Numbers \[GR\], and MeSH Terms \[MH\].

-   In addition to not having abstracts, approximately two percent of
    OLDMEDLINE citations do not have a title. These factors reduce the
    number of access points for searchers.

**NOTE**: In late 2005, NLM began an OLDMEDLINE Other Term-to-MeSH
mapping project. This project maps those terms to current MeSH
vocabulary and will be maintained each year during year end processing.
NLM estimates that approximately 92% of the OLDMEDLINE citations have at
least one MeSH term (as of Dec. 2005). All current MeSH headings added
to these records have been added as *major* MeSH headings. Additional
work on this project will continue. See
<http://www.nlm.nih.gov/databases/databases_oldmedline.html> for
additional information.

**[N]{.underline} [O]{.underline} [T]{.underline} [E]{.underline}
[S]{.underline}**

## Automatic term mapping

-   Automatic Term Mapping is a process the PubMed search engine uses
    every time a word or words are typed into the search box and a
    search is initiated.

-   Note: Automatic Term Mapping does [not]{.underline} apply when:

    -   Truncation is used in the search

    -   Quotation marks are used in the search string

    -   Tags are used to indicate the field to be searched (eg., \[TA\]
        or \[journal\] or \[MESH:NOEXP\])

-   The Automatic Term Mapping process consists of three steps in which
    the PubMed search engine compares what is in the search box to three
    separate tables. Those steps, in order, are:

    1.  MeSH/publication types

    2.  Journal Titles

    3.  Author

The DETAILS box in PubMed will show you EXACTLY how Automatic Term
Mapping was applied to your search.

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8333333333333334in"   Practice Safe Searching: Always check the details box.
  height="0.9208333333333333in"}                         

  ------------------------------------------------------ ----------------------------------------------------------

-   [Step one: MeSH / Publication Types / Substance Names]{.underline}

-   Whenever a word or words are typed into the search box, PubMed's
    search engine looks at the words as a group and compares them to a
    table of MeSH terms (descriptors and qualifiers), publication types,
    and substance names.

-   If it finds a match, the appropriate MeSH/pub type/substance name is
    applied, a text word search (the term in the search box) is added to
    the search using OR, and the search is executed. No further steps
    are taken. Effective Nov. 22, 2004, an additional piece may be added
    to the search ("xxxxxx"\[TIAB\] NOT MEDLINE\[sb\]") in order to
    enhance retrieval of non-MEDLINE citations.

-   If it does not find a match with a MeSH term and/or publication type
    and/or substance name, it moves on to step two.

Example: Type "nosebleed" into the PubMed search box. The Details box
will show how Automatic Term Mapping translated the search:

![](media/image11.png){width="5.363888888888889in"
height="2.4166666666666665in"}

Note: If the search term maps both to a MeSH term and a publication
type, the mapping will include both. See the Details box for a search on
"practice guidelines":

![](media/image12.png){width="4.469444444444444in" height="2.34375in"}

-   [Step two: Journal titles]{.underline}

-   If there has been no match with a MeSH/publication type/substance
    name (step one), then PubMed's search engine compares the words in
    the search box to a table of journal titles.

-   If it finds a match, the appropriate journal title is applied and
    the search is executed. No further steps are taken.

-   If it does not find a match with a journal title, it moves on to
    step three.

Example: Type "tuber lung dis" as the search and PubMed will
automatically map this to \"Tuber Lung Dis\"\[Journal\]. All the
citations will be from the journal *Tubercle and Lung Disease.* This
happens because "tuber lung dis" is not a MeSH term or publication type
(so no match in step one) but it is the official Medline abbreviation
for that journal (match in step two).

> Example: If I want to find all the citations from the journal *Brain*
> and I type "brain" into the search box, the details will show:
> (\"brain\"\[MeSH Terms\] OR brain\[Text Word\]). Why? "Brain" maps to
> a MeSH term. PubMed stops the Automatic Term Mapping process because
> it found a MeSH term in step one. It will run the search. To turn off
> the Automatic Term Mapping and have PubMed retrieve citations from the
> journal, type "chest\[journal\]" into the search box and run the
> search. Now, PubMed is told which field to search.

-   [Step three: author names]{.underline}

-   If there has been no match with a MeSH term or publication type and
    no match with a journal title, then PubMed's search engine compares
    what is written in the search box to a table of author names.

-   If there is a match, the appropriate author name is applied and the
    search is executed.

> Example: Type "martini r" into the search box and the Details box will
> show the search has been translated to "martini r\[Author\]".
>
> Example: I'm looking for articles written by Treat. I don't know
> anything more than that. I type "treat" into the search box in PubMed
> and then check the Details box to find the search has been translated
> into: (\"therapy\"\[MeSH Subheading\] OR treat\[Text Word\]). Why?
> Treat maps to the MeSH qualifier "therapy" and, once that mapping has
> occurred, PubMed thinks the search has been successfully mapped and
> nothing further occurs. To force PubMed to find the author name Treat,
> I type "treat\[author\]" into the search box to turn off the Automatic
> Term Mapping and look for "treat" in the author field.

-   If there is not match, one of two things may happen:

    1.  If there is only one word in the search box and there have been
        no matches with MeSH/publication type or journal title or author
        name, then a general All Fields search is run.

    2.  If there are several words in the search box, PubMed will ignore
        the word that is furthest to the right and apply Automatic Term
        Mapping to the remaining words. This lopping will continue,
        always from the right hand side, until there is either a
        suitable match made or there are no matches to be made (at which
        time an All Fields search will be done).

-   What if Automatic Term Mapping isn't doing what I want it to do?

> There are numerous ways to remedy this. Here are three:

1.  Direct PubMed to the field you want searched by using a field tag.

2.  Edit the search directly in the Details box, inserting the more
    appropriate MeSH terms or redirecting the search to a particular
    field.

3.  Use quotation marks to search for a particular phrase and turn off
    Automatic Term Mapping.

-   What are the advantages of Automatic Term Mapping?

    -   Searchers do not have to look first for the MeSH term and then
        run the search. It's done automatically.

    -   Even novice searchers will find relevant information -- and be
        taking advantage of MeSH searching without even knowing it.

    -   Searchers do not have to remember to append the text word search
        onto their search string in an effort to get at the citations
        added most recently to the database (sometimes referred to as
        "pre-Medline" citations). This is done automatically.

**Direct MeSH Searching**

It is possible to search using MeSH terminology without using either the
Entrez MeSH Database or Automatic Term Mapping. This can be accomplished
in a number of ways:

1.  Construct a search using the Preview/Index function. Select the
    appropriate field from the "All Fields" drop-down menu and use the
    Index function to help select terms.

2.  Construct the search using the Limits function of PubMed. Select the
    appropriate field from the "All Fields" drop-down menu on the Limits
    screen.

3.  Construct the search using appropriate field tags in either the
    Search box or the Details box. Appropriate field tags may include
    the following:

> \[mh\]  MeSH heading
>
> \[majr\]  MeSH Major heading
>
> \[mh:noexp\]  MeSH heading, do not explode
>
> \[majr:noexp\]  Mesh Major heading, do not explode

4.  Add terms to a search by using the hyperlinked MeSH terms from the
    Citation display format for an indexed citation.

# Searching With Field Tags

-   Search fields can be specified using PubMed's search field tags. A
    list of the available field names, abbreviation, and brief field
    descriptions may be found in the PubMed Help under Search Field
    Descriptions and Tags. Abbreviations are listed below with a brief
    description.

-   Each search term should be followed with the appropriate search
    field tag, indicating which field will be searched. The search field
    tag must follow the term. You cannot prequalify a term. The term
    must be post qualified.

> Correct entry: aromatherapy \[mh\]
>
> Incorrect entry: \[mh\] aromatherapy

-   Search field tags must be enclosed in **square** brackets \[ \]

-   Case and spacing do not matter: ice\[mh\] = Ice \[mh\] = ICE \[MH\]

## Search Rules and Syntax

-   The Boolean operators AND, OR, NOT still must be entered in
    uppercase letters.

-   Boolean connectors are processed left to right

-   Nesting of search terms is possible. To change the order in which
    terms are processed, enclose the concept(s) in parentheses. The
    terms inside the set of parentheses will be processed as a unit and
    then incorporated into the overall strategy. This is called nesting.

    Example: shoulder joint \[mh\] AND **(**baseball\[mh\] OR hockey
    \[mh\]**)** AND arthroscopy \[mh\]

## 

## Search Field Abbreviations

+------------+---------------------+---------------+------------------+
| **AUTHOR** | **SUBJECT**         | **JOURNAL**   | **OTHER**        |
+------------+---------------------+---------------+------------------+
|            |                     |               |                  |
+------------+---------------------+---------------+------------------+
| \[AU\]     | \[MH\] MeSH Terms   | \[TA\]        | \[SI\] Secondary |
| Author     |                     | Journal Title | Source           |
| Name       |                     |               |                  |
+------------+---------------------+---------------+------------------+
| \[AD\]     | \[MAJR\] Mesh Major | \[EDAT\]      | \[UID\] Unique   |
| A          | Topic               | Entrez Date   | Identifier       |
| ffiliation |                     |               |                  |
+------------+---------------------+---------------+------------------+
| \[1AU\]    | \[MHDA\] MeSH       | \[DP\]        | \[FI\] Filter    |
| First      | heading date added  | Publication   |                  |
| named      |                     | Date          |                  |
| author     |                     |               |                  |
+------------+---------------------+---------------+------------------+
| \[FAU\]    | \[SH\] MeSH         | \[VI\] Volume | \[PS\] Personal  |
| Full       | Subheading          |               | Name as          |
| author     |                     |               | Subject\*        |
| name       |                     |               |                  |
+------------+---------------------+---------------+------------------+
| \[LASTAU\] | \[PT\] Publication  | \[IP\] Issue  | \[SB\] Subset    |
| Last named | Type                |               |                  |
| author     |                     |               |                  |
+------------+---------------------+---------------+------------------+
| \[CN\]     | \[RN\] EC/Registry  | \[PG\]        | \[LA\] Language  |
| Corporate  | Number              | Pagination    |                  |
| author     |                     |               |                  |
+------------+---------------------+---------------+------------------+
|            | \[NM\] Substance    | \[LA\]        | \[OT\] Other     |
|            | Name                | Language      | term             |
+------------+---------------------+---------------+------------------+
|            | \[PA\]              |               | \[TW\] Text      |
|            | Pharmacologic       |               | Words            |
|            | action MeSH term    |               |                  |
+------------+---------------------+---------------+------------------+
|            |                     |               | \[TI\] Title     |
|            |                     |               | words            |
|            |                     |               |                  |
|            |                     |               | \[TIAB\] Words   |
|            |                     |               | in title or      |
|            |                     |               | abstract         |
+------------+---------------------+---------------+------------------+

> \* \[PS\] is the only Field Qualifier NOT included in PubMed Limits.

### Author Searching \[AU\]

-   Use \[au\] tag. Examples: o'brien j \[au\] ; pizza\[au\]

-   If the first initial is included, PubMed automatically truncates the
    author's name to account for varying initials. To turn
    [off]{.underline} automatic truncation of an author's name:

    \(1\) surround the author's name with double quotes and use the
    \[au\] search tag; or,

    \(2\) place an @ sign after the author's first initial

![](media/image13.png){width="5.995138888888889in"
height="1.1159722222222221in"}

[NOTE]{.underline}: For records created 1966-1983, the number of authors
allowed per citation was not limited. Between 1984-1995, only 10 authors
were allowed, with "et al" designating the existence of additional
authors. From 1996-1999, the number of authors allowed was increased to
25 (the first 24 named authors, the last named author, followed by "et
al"). And, in 2000, the restriction on the number of authors was
removed.

**Full Author Names** **\[FAU\]** are included in MEDLINE records in the
FAU field as of 2002. The field is searchable as of May 2005.

  ----------------------------------------------------- -----------------------------------
  ![](media/image14.png){width="2.7805555555555554in"   Author names may be entered in
  height="1.375in"}                                     regular or inverted order: Richard
                                                        Buckley or Buckley, Richard. The
                                                        comma between last name and first
                                                        name is not required but may be
                                                        needed in some cases to distinguish
                                                        a surname from a given name.
                                                        Example: Ryan, James with the comma
                                                        to distinguish James Ryan from Ryan
                                                        James.

  ----------------------------------------------------- -----------------------------------

[NOTE]{.underline}: Full author names are entered into the MEDLINE
record when they appear in the author position of an article, usually on
the title page of the article. If only the last name and initials appear
in the author position, then only the last name and initials will be
entered, even if a form of the fuller name appears elsewhere in the
article or in the Table of Contents for the journal.

**First Named Author \[1AU\]** or **Last Named Author \[LASTAU\]:** It
is now possible to limit author searching to the first named personal
author or the last named personal author on a citation. These options
are also available in the Single Citation Matcher and as a Sort option.

Note: pizza\[au\] and pizza\[1au\] and pizza \[lastau\] are different
searches.

### 

### Corporate Author \[CN\]

-   Identifies the corporate authorship of an article.

-   Corporate names display *exactly* as they appear in the journal.

-   This field was added to records in 2001. Prior to 2001, corporate
    author information was contained only at the end of the title field.

-   Citations indexed pre-2000 and some citations indexed in 2000-2001
    retain corporate authors at the end of the title field. For
    comprehensive searches, consider including terms and/or words
    searched in the title field \[ti\].

-   Corporate author names are not standardized, edited, or translated
    into English by NLM. \[The exception to this is Arabic, Chinese,
    Hebrew, and Japanese -- NLM will input a translation of the
    corporate author into the CN field.\]

### Personal Name as Subject \[PS\]

-   Use the \[ps\] tag to search for citations to articles *about* a
    named individual. The name is searched in the same format as for
    authors.

-   This field is not available in either Limits or in the Preview/Index
    function in PubMed. The only way to search this is to use the \[PS\]
    tag.

-   FPS: This field displays in the MEDLINE format in PubMed and
    contains the full name of the subject of the article for citations
    with a date of publication beginning in 2002. The FPS field is not
    currently searchable, however.

> Example: Use bush gw \[ps\] for articles *about* George W Bush

![](media/image15.png){width="5.9944444444444445in"
height="2.667361111111111in"}

### Affiliation \[AD\]

-   Traditionally, this includes the institutional affiliation and
    address (including email address) of the **first named author** of
    the article as it appears in the journal.

-   This field can be used to search for work done at specific
    institutions, but it will only retrieve citations that actually have
    the institutional name appearing in the address.

> Example*:* cleveland \[ad\] AND clinic \[ad\]
>
> Example: Cleveland clinic \[ad\]

###  Grant Number \[GR\]

-   Grant and contract numbers are also searchable using the \[gr\]
    search field tag.

> Example: LM05545 \[gr\]

  ------------------------------------------------------ -----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8333333333333334in"   Grant and contract numbers display in the GR field of the
  height="0.9208333333333333in"}                         MEDLINE format and in the Citation Format. In the Citation
                                                         Format, these may appear as hyperlinks.

  ------------------------------------------------------ -----------------------------------------------------------

-   This field was introduced in 1981 and is comprised of three parts:

1.  **Number** contains the research grant or contract number (or both)
    that designates financial support by any agency of the United States
    Public Health Service or any institute of the National Institutes of
    Health. The data are recorded exactly as they appear in the
    published article; there is no attempt to standardize the numbers.

2.  **Acronym** contains the 2-letter grant acronym.

3.  **Agency** contains the institute acronym or mnemonic.

-   NOTE: As of June 2, 2005, Wellcome Trust is now added if an author
    acknowledges that the research was supported financially by this
    organization. The organization name is typically cited without a
    specific grant number.

> Example: "Wellcome Trust"\[gr\]

  ------------------------------------------------------ -----------------------------------------------------------
  ![](media/image16.jpeg){width="0.8298611111111112in"   The three pieces of the grant number (LM05545 - number,
  height="0.9173611111111111in"}                         LM - acronym, and NLM - institute mnemonic) are each
                                                         individually searchable using the \[gr\] tag.

                                                         More precise retrieval results from searching on the
                                                         institute acronym (e.g., LM for NLM sponsored grants),
                                                         rather than the institute mnemonic (e.g., NLM) because
                                                         mnemonics may also occur in the street or email portion of
                                                         addresses.

                                                         In cases where the grant acronym is also a state postal
                                                         abbreviation (e.g., CA), search both the acronym and the
                                                         mnemonic (e.g., ca \[gr\] and nci \[gr\]).
  ------------------------------------------------------ -----------------------------------------------------------

### 

### Registry Number \[RN\]

-   83-86-3 (Phytic Acid)

![](media/image17.png){width="5.996527777777778in"
height="1.3784722222222223in"}

### 

### Substance Name \[NM\] 

-   Searching the substance name allows for more specific searching of
    drug & substance names.

![](media/image18.png){width="5.996527777777778in" height="2.53125in"}

### Text Words \[TW\]

-   Terms or numbers that are searched with the Text Words \[tw\] field
    tag will be searched in the following fields:

    -   Title

    -   Abstract

    -   MeSH headings and Subheading

    -   Other Term \[OT\] field of OLDMEDLINE citations

    -   Chemical Names of Substances

    -   Secondary Source Identifier

    -   Personal Name as Subject

### 

### Title Word Searching \[TI\] or Words in Title or Abstract \[TIAB\]

-   Enter significant terms (numbers, too) from the title of an article.

-   Each word must be followed by the \[TI\] search field tag.

-   Words should be combined with the AND operator.

Example: I'm looking for an article. The title is *Memory improvement
following cardiac transplantation.*

Search: memory \[ti\] AND improvement \[ti\] AND cardiac \[ti\] AND
transplantation \[ti\]

**Result:**

![](media/image19.wmf){width="5.995833333333334in"
height="1.0131944444444445in"}

  ------------------------------------------------------ -----------------------------------------------------------
  ![](media/image16.jpeg){width="0.8298611111111112in"   Consider using the Single Citation Matcher available from
  height="0.9173611111111111in"}                         the sidebar. When using Single Citation Matcher, you do not
                                                         have to tag each title word. Or, choose Title Word from
                                                         Limits, which also eliminates the need to qualify each word

  ------------------------------------------------------ -----------------------------------------------------------

### 

### Limiting to citations with abstracts

-   Use the value: hasabstract

+-----------+----------------------------------------------------------+
| ![](med   | Do ***not*** use a field tag; just use the search value. |
| ia/image1 |                                                          |
| 6.jpeg){w | Example: baseball AND hasabstract                        |
| idth="0.8 |                                                          |
| 298611111 |                                                          |
| 111112in" |                                                          |
| hei       |                                                          |
| ght="0.91 |                                                          |
| 736111111 |                                                          |
| 11111in"} |                                                          |
+-----------+----------------------------------------------------------+

  ------------------------------------------------------ -----------------------------------------------------------
  ![](media/image16.jpeg){width="0.8298611111111112in"   The "only items with abstracts" selection in Limits makes
  height="0.9173611111111111in"}                         restricting to only items with abstracts easy.

  ------------------------------------------------------ -----------------------------------------------------------

### 

### Publication Type \[PT\]

-   Describes the type of material the citation represents

-   Examples: Twin Study, News, Review, Clinical Trial, Retracted
    Publication, Letter

-   Use the \[pt\] tag for searching

> Example: vascular diseases \[majr\] AND twin study \[pt\]

+----------+-----------------------------------------------------------+
| ![](     | See <http://www.nlm.nih.gov/mesh/pubtypes2005.html> from  |
| media/im | the NLM MeSH section for a listing of all available       |
| age10.jp | publication types for 2005. Includes scope notes.         |
| eg){widt |                                                           |
| h="0.833 | PubMed's **Help** also includes a listing of all          |
| 33333333 | available Publication Types.                              |
| 33334in" |                                                           |
| height   |                                                           |
| ="0.9208 |                                                           |
| 33333333 |                                                           |
| 3333in"} |                                                           |
+----------+-----------------------------------------------------------+

+----------+-----------------------------------------------------------+
| ![](     | > All available publication types may be viewed by using  |
| media/im | > the **Preview/Index** function of PubMed. Access the    |
| age16.jp | > Preview/Index page, select "Publication Type" from the  |
| eg){widt | > All Fields drop down menu and then click on Index.      |
| h="0.833 |                                                           |
| 33333333 |                                                           |
| 33334in" |                                                           |
| height   |                                                           |
| ="0.9166 |                                                           |
| 66666666 |                                                           |
| 6666in"} |                                                           |
+----------+-----------------------------------------------------------+

### Other Term \[OT\]

-   Pertains to OLDMEDLINE citations.

-   The OT field contains the original MeSH Headings assigned at the
    time the records were first established prior to 1966. These
    headings have not been updated and may not match current MeSH
    headings and subheadings.

-   For additional information on the OT field, see the OLDMEDLINE
    section of this manual or the *NLM Technical Bulletin* article at
    <http://www.nlm.nih.gov/pubs/techbull/so03/so03_oldmedline.html>

-   The OT field is also searchable with the \[TW\] tag.

### Language \[LA\]

-   The language in which the article is written.

-   First three letters of the language may be used as an abbreviation
    when searching.

(There are a few exceptions. Example: JPN for Japanese)

-   Language values may also be spelled out.

Examples: common cold \[mh\] AND chi \[la\]

common cold \[mh\] AND chinese \[la\]

common cold \[mh\] AND por \[la\]

common cold \[mh\] AND portuguese \[la\]

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image16.jpeg){width="0.8298611111111112in"   Commonly-searched languages are available from the
  height="0.9173611111111111in"}                         pull-down menu in Limits. The full list of languages can
                                                         be viewed and searched using the Preview/Index feature

  ------------------------------------------------------ ----------------------------------------------------------

### 

### Journal Name \[TA\]

-   Search for journals using the full journal name, or the MEDLINE
    abbreviation, or the ISSN.

Examples: journal of biological chemistry \[ta\]

j biol chem \[ta\]

0021-9258 \[ta\]

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image16.jpeg){width="0.8298611111111112in"   When searching journal titles, use the Journal Database or
  height="0.9173611111111111in"}                         the Single Citation Matcher. There is less opportunity for
                                                         error with these methods.

  ------------------------------------------------------ ----------------------------------------------------------

### 

### Entrez Date \[EDAT\]

-   The Entrez Date field contains the date that the record was
    initially added to PubMed.

-   Search this in the format yyyy/mm/dd \[edat\]

> Example: 1999/07/10 \[edat\]

-   Month and day are optional:

> Example: 1999 \[edat\]
>
> Example: 1999/07 \[edat\]

  ------------------------------------------------------ -----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8333333333333334in"   The Entrez Date will remain unchanged and is not updated to
  height="0.9208333333333333in"}                         reflect the date a publisher-supplied record is elevated to
                                                         in process, or when an in process record is elevated to
                                                         MEDLINE status.

  ------------------------------------------------------ -----------------------------------------------------------

### Publication Date \[DP\]

-   The date that the article was published in the format of YYYY/MM/DD.

-   Use the \[dp\] search tag.

-   Month and day are optional.

> Examples:
>
> 1984/10/06 \[dp\]
>
> 1984/10 \[dp\]
>
> 1984 \[dp\]

## 

### Date Ranging (EDAT and DP)

-   The colon (:) is used between ranging values.

-   To search for Publication Date between 1993 and 1997, enter:

> 1993:1997 \[dp\]

-   Proper date format is YYYY/MM/DD

-   EDAT = Entrez Date. The Entrez Date is set to the Publication Date
    on citations before September 1997, when this field was first added
    to PubMed.

-   DP = Date of Publication

> Example 1:
>
> Search for citations entered into PubMed from Jan 16, 1998 to Feb 13,
> 1998
>
> 1998/01/16:1998/02/13 \[edat\]
>
> Example 2:
>
> Search for citations published in January or February 1998
>
> 1998/01:1998/02 \[dp\]

+-------------+--------------------------------------------------------+
| ![](medi    | Use the following format to search X days, months or   |
| a/image16.j | years immediately preceding today's date where X =     |
| peg){width= | numeric value:                                         |
| "0.82986111 |                                                        |
| 11111112in" | -   "last X days"\[dp\]                                |
| height="    |                                                        |
| 0.917361111 | -   "last X months"\[dp\]                              |
| 1111111in"} |                                                        |
|             | -   "last X year"\[dp\]                                |
+-------------+--------------------------------------------------------+

## 

### Volume \[VI\] Issue \[IP\] Pagination \[PG\]

  ------------------------------------------------------ -----------------------------------------------------------
  ![](media/image16.jpeg){width="0.8298611111111112in"   Consider using the Single Citation Matcher available from
  height="0.9173611111111111in"}                         the sidebar. When using Single Citation Matcher, you do not
                                                         have to tag each volume, issue, or page.

  ------------------------------------------------------ -----------------------------------------------------------

### Secondary Source Identifier \[SI\]

-   Beginning with the summer of 2005, NLM includes the
    ClinicalTrials.gov identifier number in the SI field when that
    information appears in the original publication as recommended by
    the International Committee of Medical Journal Editors (ICMJE).

-   SI field also identifies secondary source databanks and accession
    numbers of molecular sequences discussed in MEDLINE articles.

-   Currently, there are six databases registering molecular sequence
    data:

  --------------------- -------------------------------------------------
  GDB                   Johns Hopkins University Genome Data Bank

  GENBANK               GenBank (NIH)

  OMIM                  Online Mendelian Inheritance in Man

  PDB                   Protein Data Bank

  PIR                   Protein Identification Resource

  SWISSPROT             Protein Sequence Database
  --------------------- -------------------------------------------------

-   The field is composed of the source followed by a slash followed by
    an accession number and can be searched with one or both components.

    Examples: GENBANK/AF306859

    SWISSPROT/P13209

    ClinicalTrials.gov/NCT00000419

    Sesarch: genbank\[SI\]

    AF306859\[SI\]

    genbank/AF001892 \[si\].

-   Data in this field is sorted first by databank name and then by
    accession number.

```{=html}
<!-- -->
```
-   The SI field and the Entrez sequence database links are not linked.
    The PubMed links to these databases are created from the reference
    field of the GenBank or GenPept flatfile. These references include
    citations that discuss the specific sequence presented in these
    flatfiles.

### Unique Identifier Searching \[UID\]

-   To search using the PubMed Unique Identifier (PMID), type in the
    number with or without the search field tag \[uid\].

    Example: 11073054

-   You can search for several Unique Identifier numbers by entering
    each number in the query box separated by a space, PubMed will OR
    them together. Do ***not*** enter the OR connector.

    Example: 7715939 11073054

+-----------+----------------------------------------------------------+
| Unique    | ![](media/image20.png){width="5.082638888888889in"       |
| Id        | height="3.1875in"}                                       |
| entifiers |                                                          |
|           |                                                          |
| as        |                                                          |
| entered   |                                                          |
| in the    |                                                          |
|           |                                                          |
| query     |                                                          |
| box.      |                                                          |
|           |                                                          |
| PubMed    |                                                          |
| finds the |                                                          |
| 2         |                                                          |
| c         |                                                          |
| itations. |                                                          |
+-----------+----------------------------------------------------------+

-   To search for a Unique Identifier **in combination with other
    terms** you ***must*** use the search field tag \[uid\].

> Example: smith \[au\] AND (10403340 \[uid\] OR vaccines \[mh\])

# Subset \[SB\]

-   Allows you to limit your search to various PubMed subsets.

-   Use the \[sb\] tag for searching

-   Available values include:

+-----------------------+-----------------------+----------------------+
| **Level of            | **Subject** Subsets   | **Journal** Subsets  |
| processing**          |                       |                      |
|                       |                       |                      |
| (**Status**) Subsets  |                       |                      |
+-----------------------+-----------------------+----------------------+
|                       |                       |                      |
+-----------------------+-----------------------+----------------------+
| -   medline \[sb\]    | -   aids \[sb\]       | -   medline pmc      |
|                       |                       |     \[sb\]           |
+-----------------------+-----------------------+----------------------+
| -   in process \[sb\] | -   bioethics \[sb\]  | -   free full text   |
|                       |                       |     \[sb\]           |
+-----------------------+-----------------------+----------------------+
| -   publisher \[sb\]  | -   cam \[sb\]        | -   loprov*medlib*   |
|                       |     (Complementary    |     \[sb\]           |
|                       |     Medicine)         |                      |
+-----------------------+-----------------------+----------------------+
| -   all \[sb\]        | -   history \[sb\]    | -   jsubset*name*    |
+-----------------------+-----------------------+----------------------+
| -   p                 | -   space \[sb\]      |                      |
| ubmednotmedline\[sb\] |                       |                      |
+-----------------------+-----------------------+----------------------+
| -   OLDMEDLINE        | -   systematic \[sb\] |                      |
|                       |     (Systematic       |                      |
|                       |     Reviews)          |                      |
+-----------------------+-----------------------+----------------------+
|                       | -   tox \[sb\]        |                      |
|                       |     (Toxicology)      |                      |
+-----------------------+-----------------------+----------------------+

### Limiting to published journal indexes

-   The following values are available to limit to published (or
    previously published) journal indexes such as *International Nursing
    Index.*

-   Do [not]{.underline} use a field tag; just use the search value 
    jsubset*code*

-   Do [not]{.underline} confuse JOURNAL subsets with SUBJECT subsets

  ---------- ---------------------------------------------------------------
  **Subset   **Journal/Citation Subset**
  Code**     

  AIM        [Abridged Index Medicus](http://www.nlm.nih.gov/bsd/aim.html)
             is a list created 20 years ago of 120 core clinical English
             language journals that corresponds to \"Core clinical
             journals\" subset in Limits.

  D          Dentistry journals

  E          Citations from bioethics journals or selected bioethics
             citations from other journals

  H          Health adminstration journals, non-Index Medicus

  IM         Index Medicus journals

  K          Consumer health journals, non-Index Medicus

  N          Nursing journals

  Q          History of medicine journals and selected citations from other
             journals

  S          Citations from space life sciences journals and selected space
             life sciences citations from other journals

  T          Health technology assessment journals, non-Index Medicus

  X          AIDS/HIV journals (selected citations from other journals
             1980-2000)
  ---------- ---------------------------------------------------------------

# Filter \[filter\] or \[sb\]

-   Technical tags used by LinkOut providers to qualify holdings.

-   Use the following query to find all the LinkOut links in PubMed:

> **Loall \[filter\]**

-   You may also use Preview/Index to browse the index of LinkOut
    providers. Select Filter from the All Fields pull-down menu, enter
    "lo" in the adjacent search box, and then click "Index." PubMed will
    display an alphabetic list of all the LinkOut entries.

-   If a library has set up LinkOut for Libraries and linked their
    electronic journal collection and/or their DOCLINE SERIAL HOLDINGS
    to PubMed, it is possible to limit a search to just those holdings
    by using a filter. The filter begins with **loprov** and, following
    that are the letters assigned to that institution (their code).

> Examples:
>
> **loprovmghlib** will limit to the LinkOut holdings of the
> Massachusetts General Hospital Treadwell Library
>
> **loprovumasslib** will limit to the LinkOut holdings of the U Mass
> Medical School library
>
> To find a library's code, click on LinkOut on the blue sidebar on the
> PubMed page. Then, click on "All Providers" to see a list.

-   There are numerous other filters available in PubMed. These can be
    seen by using the Preview/Index function. Select "Filter" from the
    All Fields drop down menu, enter lo in the text box, and click
    "Index." PubMed will display an alphabetic listing of all the
    available fields.

-   The easiest way to set Filters in PubMed is to use My NCBI.

Use search field tags when doing these exercises. Remember you can use
the History feature to obtain search numbers to combine searches.

1\. Find references to articles discussing decision-making by nurse
practitioners. The phrase decision-making should be in the title.

2\. Find references to articles about Winston Churchill.

3\. Find references to articles indexed with the MeSH headings for video
display terminals and carpal tunnel syndrome. Use the Related Articles
feature to find similar articles. Combine the list of Related Articles
with the publication type, Review.

4\. Using the MeSH Browser, find citations to articles about the
prevention of chickenpox or measles during pregnancy. Combine these
results to retrieve English language articles that have abstracts on the
PubMed citation.

Extra Credit Problems (not included in the Suggested Answers that
follow):

1\. Find information about doctors as patients.

2\. Find information in PubMed regarding the effectiveness of DARE
programs.

**Suggested Answers**

1\. Find references to articles discussing decision-making by nurse
practitioners. The phrase decision-making should be in the title.

![](media/image21.png){width="6.510416666666667in"
height="3.3541666666666665in"}

2\. Find references to articles about Winston Churchill.

> ![](media/image22.png){width="4.104166666666667in"
> height="0.2604166666666667in"}

3\. Find references to articles indexed with the MeSH headings for video
display terminals and carpal tunnel syndrome. Use the Related Articles
feature to find similar articles. Combine the list of Related Articles
with the publication type, Review. (Hint: Use History.)

History screen:

![](media/image23.png){width="5.635416666666667in"
height="2.5833333333333335in"}

> Final History screen:

![](media/image24.png){width="6.497222222222222in"
height="2.328472222222222in"}

4\. Using the MeSH Browser, find citations to articles about the
prevention of chickenpox or measles during pregnancy. Combine these
results to retrieve English language articles that have abstracts on the
PubMed citation.

Detailed Display screen for the MeSH term Chickenpox with the subheading
prevention & control selected:

+-----+----------------------------------------------------------------+
| Cl  | ![](media/image25.png){width="5.445833333333334in"             |
| ick | height="2.817361111111111in"}                                  |
| on  |                                                                |
|     |                                                                |
| *   |                                                                |
| *Ad |                                                                |
| d** |                                                                |
| but |                                                                |
| ton |                                                                |
|     |                                                                |
| to  |                                                                |
| be  |                                                                |
| gin |                                                                |
| to  |                                                                |
|     |                                                                |
| bu  |                                                                |
| ild |                                                                |
| y   |                                                                |
| our |                                                                |
|     |                                                                |
| str |                                                                |
| ate |                                                                |
| gy. |                                                                |
+-----+----------------------------------------------------------------+

Next, look up measles and display the detailed screen. Select the
prevention & control subheading:

![](media/image26.png){width="4.705555555555556in" height="2.7625in"}

# Discipline Searching

PubMed has a number of options that make searching in specific
disciplines simple. An obvious tool for this kind of searching is the
Journal/Citation Subsets menu found on the Limits Screen:

![](media/image27.jpeg){width="5.998611111111111in"
height="3.1680555555555556in"}

Discipline/Topic Subset choices are

-   **AIDS Subset** - This subset strategy was created to facilitate
    searching for subjects in the area of AIDS. It is based on search
    strategies used for creating NLM\'s AIDSLINE® database. This subset
    can also be used in a search as **aids \[sb\].**

-   **Bioethics Subset** - This subset strategy was created by NLM and
    the Kennedy Institute of Ethics, Georgetown University to facilitate
    searching for citations to articles in the area of bioethics. This
    subset can also be used in a search as **bioethics \[sb\].**

-   **Cancer Subset** -- This subset strategy was created by NLM and the
    National Cancer Institute to aid in searching for citations to
    cancer-related articles. This subset can also be used in a search as
    **cancer \[sb\].**

-   **Complimentary Medicine** -- This subset strategy was created by
    NLM and that National Center for Complementary and Alternative
    Medicine (NCCAM) and is designed to limit a search to citations in
    the area of complimentary and alternative medicine. This subset can
    also be used in a search as **cam \[sb\].**

-   **Dental Journals Subset** -- This subset can also be used in a
    search as **jsubsetd**.

-   **History of Medicine Subset** - This subset strategy was created by
    NLM\'s History of Medicine Division to facilitate searching for
    subjects in the history of medicine. This subset can also be used in
    a search as **history \[sb\].**

-   **Nursing Journals Subset --** This subset strategy was created
    using the titles found in the *International Nursing Index*
    (discontinued in 2000). This subset can also be used in a search as
    **jsubsetn.**

-   **Space Life Sciences Subset** - This subset strategy was developed
    by NLM and the NASA SPACELINE Office and is intended to retrieve
    citations of interest to those working in the field of space life
    sciences research. This subset can also be used in a search as
    **space \[sb\].**

-   **Toxicology Subset** - This subset strategy was created by NLM\'s
    Specialized Information Services to facilitate searching for
    subjects in the area of toxicology. This subset can also be used in
    a search as **tox \[sb\].**

PubMed also offers other powerful tools for use by the researcher
working in a specific discipline: natural language searching, specific
MeSH headings and MeSH subheadings. Following are instructions from some
sample disciplines.

## Veterinary Medicine Discipline Searching

There is no veterinary medicine subset in limits, but MEDLINE indexes
more than 80 titles directly relevant to the veterinary sciences.
However, the most commonly used method of searching veterinary topics,
limiting to animal subjects is a wildly inaccurate strategy since this
tactic will retrieve citations to articles on the testing of
human-oriented applications upon animal subjects. There are other
approaches that are more concise if the searcher is seeking material for
the treatment of animals.

### Natural Language and Vet Med Searching

Adding a specific animal-type to a search increases the chances of
getting appropriate citations, although, as with the test subject limit,
human applications will not be excluded:

> EXAMPLE:
>
> Mitral regurgitation AND (dog OR canine)
>
> Or
>
> Mitral regurgitation AND (dog\* or canine\*)
>
> \[The truncation is to catch plurals; however, the advanced user will
> recall that truncation turns off automatic term mapping, so there is a
> tradeoff when using wildcards.\]

A more specific strategy would include the discipline itself:

> Mitral regurgitation AND (dog\* or canine\*) AND veterinary

## 

### MeSH and VetMed Searching

The most precise way to search in most disciplines is to use MeSH
headings and subheadings. For veterinary applications, the subheading
"veterinary" (abbreviated to "VE" for the power searcher) is a useful
way to limit the retrieval set to animal applications. ("Mitral
regurgitation" maps to "Mitral Valve Insufficiency" in the MeSH
database, so a substitution will be made in the following search
strategies.)

> EXAMPLE:
>
> Mitral Valve Insufficiency/veterinary\[MeSH\]

Or for even more specificity, add an animal type:

> Mitral Valve Insufficiency/veterinary\[MeSH\] AND dogs\[MeSH\]

The advanced user can use the following short hand:

> Mitral Valve Insufficiency/ve\[mh\] AND dogs\[mh\]

This strategy could also include a free-floating subheading that will
bring in veterinary application that does not necessarily attach to the
main search topic:

> Mitral Valve Insufficiency\[mh\] AND dogs\[mh\] AND ve\[sh\]

## Nursing Discipline Searching

PubMed has a special benefit for nurses in that the Nursing Journal
Subset is built into the Limits feature. This subset contains the titles
once indexed by the *International Nursing Index (INI)*, which went out
of print in 2000. Although the *INI* is no longer in print, the Nursing
Journal Subset continues to be updated in PubMed and may be searched in
two different ways: using Limits or the search command **JSUBSETN.**

The Limits method involves selecting the Nursing Journal Subset from the
subset drop-down box in the Limits feature:

![](media/image27.jpeg){width="5.998611111111111in"
height="3.1680555555555556in"}

The search command method involves adding **jsubsetn** to the search
strategy:

Self Care AND jsubsetn

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8298611111111112in"   Not all *Index Medicus* nursing journals are included in
  height="0.9208333333333333in"}                         the Nursing Journals Subset; therefore, a search limited
                                                         in this manner will miss these journals; moreover, not all
                                                         nursing articles are published in nursing journals, so
                                                         these articles will be missed by this strategy also.

  ------------------------------------------------------ ----------------------------------------------------------

### MeSH and Nursing

For a search that extends beyond the nursing journals subset, but is
specific to the nursing profession, a search strategy can be constructed
from MeSH terms instead of using the subset limiter. There are 158
entries in the Permuted MeSH related to the terms \"Nurse,\" \"Nurses,\"
and \"Nursing,\" and the PubMed MeSH database lists 38 of these entries
directly under those terms. (This means that 38 \"Nurse, Nurses,
Nursing\" related subjects may be searched at once by taking advantage
of MeSH terms and PubMed\'s automatic explosion of terms.) Other
combinations may be found under subjects such as \"Philosophy,
Nursing.\" These other combinations do not show up as readily in the
MeSH browser, therefore the print Permuted MeSH continues to be a
helpful tool.

#### MeSH Subheadings and Nursing

Of course not all searches about nursing information are about nursing.
Some are about nursing aspects of some topic\--a disease, or practice,
for example. MeSH is useful in this situation by giving one the ability
to modify a term with a subject heading. For instance, to get
information on care giving in the context of cancer, search on the term
\"neoplasms\" with \"nursing\" used as a subheading or modifier:

> Neoplasms/nursing\[mh\]

Or

> Neoplasms/nu\[mh\]

As with the veterinary search, the subheading "nursing" or "nu" may be
added to a strategy as a free-floating subheading:

> Neoplasms\[mh\] AND nu\[sh\]

## Allied Health Discipline Searching

Searching MEDLINE® for information relevant to allied health professions
is not as straightforward as finding literature relevant to nursing or
veterinary medicine. The large variety of occupations involved makes the
creation of a simple filter unwieldy and undesirable. This section will
show how MeSH® maps allied health professions and will aid searchers
building queries that effectively retrieve information written (1) about
and (2) for these occupations.

As a result of a division between professional and paraprofessional
occupations, MeSH has two major categories that are further subdivided
into allied health practice: Allied Health Occupations, and Allied
Health Personnel. \"Allied Health Occupations\" belongs under the
Biological Sciences/Health Occupations rubric while \"Allied Health
Personnel\" belongs under the \"Persons Category.\" The distinction is
academic: audiology is an occupation; an emergency medical technician is
a person. Consequently, there are no MeSH terms for audiologist or for
emergency medical technology. Following are the two categories and their
subordinate headings.

+-----------------------------------+-----------------------------------+
| ### Allied Health Occupations     | ### Allied Health Personnel       |
|                                   |                                   |
| Audiology                         | Animal Technicians                |
|                                   |                                   |
| Occupational Therapy              | Community Health Aides            |
|                                   |                                   |
| Physical Therapy (Specialty)      | Dental Auxiliaries                |
|                                   |                                   |
| Speech-Language Pathology         | Dental Assistants                 |
|                                   |                                   |
| Technology, Dental                | Dental Hygienists                 |
|                                   |                                   |
| Technology, Medical               | Dental Technicians +              |
|                                   |                                   |
| Technology, Radiologic            | Emergency Medical Technicians     |
|                                   |                                   |
| Teleradiology                     | Home Health Aides                 |
|                                   |                                   |
|                                   | Medical Record Administrators     |
|                                   |                                   |
|                                   | Medical Secretaries               |
|                                   |                                   |
|                                   | Medical Receptionists             |
|                                   |                                   |
|                                   | Nurses\' Aides                    |
|                                   |                                   |
|                                   | Psychiatric Aides                 |
|                                   |                                   |
|                                   | Operating Room Technicians        |
|                                   |                                   |
|                                   | Pharmacists\' Aides               |
|                                   |                                   |
|                                   | Physician Assistants              |
|                                   |                                   |
|                                   | Ophthalmic Assistants             |
|                                   |                                   |
|                                   | Pediatric Assistants              |
+-----------------------------------+-----------------------------------+

A MEDLINE search for information about a specific allied health field
would use the appropriate subcategory. For instance, to find information
regarding physician assistants. start with:

> Physician Assistants \[mh\]

The strategy indicated above can be fleshed out to create real searches
about the work of physician assistants by adding more terms, either
natural language terms or MeSH. To find out the role of physician
assistants in nephrology, start with a search strategy that looks like
this:

> Physician Assistants \[mh\] AND nephrology

Or

> Physician Assistants \[mh\] AND nephrology \[mh\]

The two searches do not, of course, exhaust the possibilities for this
simple strategy; for one or both of the search terms can be made into
major terms.

There are a number of allied health occupations (see the AMA\'s list at
http://www.ama-assn.org/ama/pub/category/2322.html), that are missing
from MeSH, for instance, recreation therapist, cytotechnologist,
perfusionist (a. k. a. perfusion therapist). To search MEDLINE for
information on these topics start with this question: may this
occupation be found in another branch of the MeSH tree? Medical
Illustration is a subcategory all by itself under \"Health
Occupations.\" While MeSH doesn\'t recognize Medical Illustration as an
Allied Health Occupation, it does recognize it as an occupation.

But what about perfusionists? MeSH recognizes \"perfusion\" but not the
therapists who do the work. Here, it is time to partially abandon MeSH;
to initiate a search for articles about perfusionists by entering
\"Perfusionist\" into the PubMed search box without any qualifiers:

> Perfusionist

The term is entered without qualifiers. PubMed searches for the word in
all fields, including titles and abstracts. All allied health queries
may be entered in this way, without the MeSH apparatus, but MeSH allows
considerable control in a search strategy. So, MeSH need not be
abandoned altogether in this kind of search. Someone interested in the
intersection of perfusion therapy and aortic aneurysm in the abdominal
region might use a combination of the natural language search above and
MeSH terminology:

> Perfusionist AND Aortic Aneurysm, Abdominal \[MH\]

This strategy finds \"perfusionist\" in title or abstract and the
aneurysm in the MeSH field. Oddly, because \"perfusionist\" is such a
specific profession, as are most allied health occupations, this usually
scattershot way of searching leads to very precise results. The
inclusion of a MeSH recognized condition or disease makes the search
even more unambiguous.

The AMA recognizes fifty-three allied health occupations, not all of
which are recognized by MeSH. But neither does the AMA recognize all
occupations that other associations or schools include in their roster
of occupations. What is important to remember is not particularly that
MeSH does not measure up, but that MEDLINE remains a great source of
bibliographic information for the allied health fields. And not a
tremendous amount of skill is required to search with PubMed: know when
to use MeSH and when to use natural language and when to use them in
tandem.

#  

## Pharmacologic Action Headings (PA) and Searching for Drug Information 

Part of this is taken from the *NLM Technical Bulletin*

See <http://www.nlm.nih.gov/pubs/techbull/ja03/ja03_papx.html> for the
entire article.

In 1996, the MeSH Tree Structure was changed so that specific
drugs/chemicals were no longer treed under a function (pharmacological
action) heading. This means that in MeSH there is no branch containing
all drugs with a particular effect (e.g., all the antioxidants).

The old PubMed MeSH browser displayed the associated drug/substance
terms under the respective action term in the hierarchical display --
even though these indentions did not really exist in the MeSH tree
structure.

Changes to PubMed:

\(1\) PubMed's MeSH Database includes only those indentions for PA terms
found in the actual MeSH tree structure -- not (as before) terms that
had the effect, but were not true indentions.

\(2\) Search with \[PA\]: A new search tag, \[PA\], and a new index of
Pharmacological Action terms been created. See this index using the
Preview/Index function in PubMed. Use of a term with this tag instructs
PubMed to OR together terms from a list made up of a PA term and the
drug/substance terms known to have that effect. This includes both MeSH
headings and terms for Supplementary Concept Records. Any MeSH terms on
the lists are searched with the no explode specification \[mh:noexp\],
so as not to include any possible indentions of the term that might not
share the pharmacologic action. Use this search method when you want to
include retrieval for all MeSH terms with a particular action. For
example: neoplasms\[mh\] AND antioxidants\[pa\]

\(3\) Pharmacologic Action Lists: To see what substances are included in
a PA list, either the NLM MeSH browser or the PubMed MeSH database may
be used.

-   In the NLM MeSH browser, enter a PA term, click "Pharmacological
    Action \[PA\]", and then click "Find exact term."

-   In the PubMed MeSH browser, enter a PA term in the search box and
    then look for the "\[pharmacological action\]" tag following the
    term in the results.

\(4\) Search with \[MH\]: Terms tagged with \[MH\] will retrieve the
term and the true indentions (due to automatic exploding of terms). This
allows searchers to retrieve citations about a drug or substance with a
specific action back through 1996.

\(5\) Search with no tag: If you enter a MeSH heading (or an entry term)
that happens to be a Pharmacologic Action Term and do not use a search
tag, PubMed will automatically search the term as \[MH\], \[PA\], and
\[TW\].

NOTE: Prior to the 1996 MeSH year, NLM treed specific drugs/substances
under the pharmacologic action MeSH heading. Indexing policy stipulates
that indexers assign the most specific heading; a broader heading is
typically not added. Therefore, citations to articles about
pharmacologic actions indexed before 1996 usually carry only the
specific drug/substance heading and not the pharmacologic action
heading. If you need comprehensive searches to include citations for
articles indexed before 1996, do a search for the substance ANDed with
the PA term as well as a search for the substance alone, i.e., do not
combine with PA term.

Some additional information about searching for drug information in
PubMed:

-   MeSH indexes drug names under their generic names (US Adopted Name),
    not their brand names. However, brand names will oftentimes map to
    the appropriate generic name. Note that MeSH favors American rather
    than British names. If a drug name does not map to a MeSH term, it
    may map to a Substance Name (Supplementary Concept Record).

> Prozac will map to the MeSH term fluoxetine.
>
> Paracetamol will map to the MeSH term acetaminophen
>
> Exelon will map to the Substance Name rivastigmine

-   A drug name typed into the search box in PubMed *may* automatically
    map to the appropriate Descriptor or Substance Name -- this may not
    happen with very new drug or substance names. Remember to check the
    Details box to see how a given term maps.

```{=html}
<!-- -->
```
-   Search by Substance Name. Enter the name of the substance in the
    search box followed by \[NM\]. This will search the "Substances"
    field in the PubMed record.

> Oxycodone\[NM\] "noradrenaline transporter"\[NM\]
>
> Analgesics\[NM\] sodium\[NM\]

-   CAS numbers may be used to search. Either input the CAS number into
    the search box and hit enter or qualify your search with the tag
    \[EC/RN number\].

> Either of these two searches will retrieve information on simvastatin:
>
> 79902-63-9
>
> 79902-63-9\[EC/RN number\]

-   Research codes may be used to search for drugs in early
    investigational stages. In many cases, this will be a text word
    search and will only be successful if the research code appears in
    the title or abstract. However, later, the research code will be an
    entry term for MeSH and will map to the appropriate drug name.

> MK-639 will map to Indinavir (Crixivan)

-   When searching for drugs that may be used to treat a particular
    condition, use the MeSH term for the condition and the subheading dt
    (drug therapy).

> Hypertension/dt

-   If a condition is caused by a drug, use the MeSH term for the
    condition along with the subheading ci (chemically induced).

> Dyskinesias/ci

-   To search for the effects of a drug on an organ or physiologic
    process, use the MeSH term for the organ or physiologic process and
    add the subheading de (drug effects). Or, combine ae (adverse
    effects -- referring to the drug causing adverse effects) with ci
    (chemically induced -- referring to a condition caused by a drug).
    Using the proper MeSH/subheading combinations can effectively narrow
    a search.

> Acetaminophen AND liver/de
>
> Heparin/ae AND thrombocytopenia/ci

## Pharmacological Actions \[PA\]

Use a known pharmacological action with \[PA\].

Example: air pollutants \[PA\]

### Pharmacological Actions found in MeSH 

  --------------------------- ----------------------- -----------------------
  Abortifacient Agents,       Abortifacient Agents,   Adhesives
  Nonsteroidal                Steroidal               

  Adjuvants, Anesthesia       Adjuvants, Immunologic  Adjuvants, Pharmaceutic

  Adrenergic Agents           Adrenergic Agonists     Adrenergic
                                                      alpha-Agonists

  Adrenergic                  Adrenergic Antagonists  Adrenergic
  alpha-Antagonists                                   beta-Agonists

  Adrenergic beta-Antagonists Adrenergic Uptake       Aerosol Propellants
                              Inhibitors              

  Affinity Labels             Air Pollutants          Air Pollutants,
                                                      Environmental

  Air Pollutants,             Air Pollutants,         Alcohol Deterrents
  Occupational                Radioactive             

  Aldosterone Antagonists     Alkylating Agents       Amebicides

  Anabolic Agents             Analgesics              Analgesics,
                                                      Non-Narcotic

  Analgesics, Opioid          Androgen Antagonists    Androgens

  Anesthetics                 Anesthetics, Combined   Anesthetics,
                                                      Dissociative

  Anesthetics, Inhalation     Anesthetics,            Anesthetics, Local
                              Intravenous             

  Angiogenesis Inducing       Angiogenesis Inhibitors Angiotensin II Type 1
  Agents                                              Receptor Blockers

  Angiotensin-Converting      Anion Exchange Resins   Antacids
  Enzyme Inhibitors                                   

  Anthelmintics               Anti-Allergic Agents    Anti-Anxiety Agents

  Anti-Arrhythmia Agents      Anti-Asthmatic Agents   Anti-Bacterial Agents

  Anti-Dyskinesia Agents      Anti-HIV Agents         Anti-Infective Agents

  Anti-Infective Agents,      Anti-Infective Agents,  Anti-Inflammatory
  Local                       Urinary                 Agents

  Anti-Inflammatory Agents,   Anti-Obesity Agents     Anti-Ulcer Agents
  Non-Steroidal                                       

  Antibiotics, Antifungal     Antibiotics,            Antibiotics,
                              Antineoplastic          Antitubercular

  Antibiotics, Combined       Anticarcinogenic Agents Anticestodal Agents

  Anticholesteremic Agents    Anticoagulants          Anticonvulsants

  Antidepressive Agents       Antidepressive Agents,  Antidepressive Agents,
                              Second-Generation       Tricyclic

  Antidiarrheals              Antidotes               Antiemetics

  Antifibrinolytic Agents     Antifoaming Agents      Antifungal Agents

  Antihypertensive Agents     Antilipemic Agents      Antimalarials

  Antimanic Agents            Antimetabolites         Antimetabolites,
                                                      Antineoplastic

  Antimutagenic Agents        Antinematodal Agents    Antineoplastic Agents

  Antineoplastic Agents,      Antineoplastic Agents,  Antineoplastic Agents,
  Alkylating                  Hormonal                Phytogenic

  Antioxidants                Antiparasitic Agents    Antiparkinson Agents

  Antiplatyhelmintic Agents   Antiprotozoal Agents    Antipruritics

  Antipsychotic Agents        Antirheumatic Agents    Antirheumatic Agents,
                                                      Gold

  Antisickling Agents         Antispermatogenic       Antithyroid Agents
                              Agents                  

  Antitreponemal Agents       Antitrichomonal Agents  Antitubercular Agents

  Antitussive Agents          Antiviral Agents        Appetite Depressants

  Appetite Stimulants         Aromatase Inhibitors    Astringents

  Biocompatible Materials     Biological Response     Bone Cements
                              Modifiers               

  Bone Substitutes            Bronchoconstrictor      Bronchodilator Agents
                              Agents                  

  Buffers                     Calcium Channel         Calcium Channel
                              Agonists                Blockers

  Carbonic Anhydrase          Carcinogens             Carcinogens,
  Inhibitors                                          Environmental

  Cardiotonic Agents          Cardiovascular Agents   Cariogenic Agents

  Cariostatic Agents          Cathartics              Caustics

  Central Nervous System      Central Nervous System  Central Nervous System
  Agents                      Depressants             Stimulants

  Chelating Agents            Chemical Warfare Agents Chemosterilants

  Chemotactic Factors         Cholagogues and         Cholinergic Agents
                              Choleretics             

  Cholinergic Agonists        Cholinergic Antagonists Cholinesterase
                                                      Inhibitors

  Cholinesterase Reactivators Chromogenic Compounds   Coagulants

  Coccidiostats               Complement Inactivators Contraceptive Agents

  Contraceptive Agents,       Contraceptive Agents,   Contraceptives, Oral
  Female                      Male                    

  Contraceptives, Oral,       Contraceptives, Oral,   Contraceptives, Oral,
  Combined                    Hormonal                Sequential

  Contraceptives, Oral,       Contraceptives,         Contraceptives,
  Synthetic                   Postcoital              Postcoital, Hormonal

  Contraceptives, Postcoital, Contrast Media          Convulsants
  Synthetic                                           

  Cross-Linking Reagents      Cryoprotective Agents   Culture Media

  Cyclooxygenase Inhibitors   Cysteine Proteinase     Cytotoxins
                              Inhibitors              

  Defoliants, Chemical        Delayed-Action          Dental Alloys
                              Preparations            

  Dental Disinfectants        Dental Impression       Dental Materials
                              Materials               

  Dental Veneers              Dentifrices             Dentin-Bonding Agents

  Deodorants                  Dermatologic Agents     Detergents

  Disinfectants               Diuretics               Diuretics, Osmotic

  Diuretics, Sulfamyl         Diuretics, Thiazide     Dopamine Agents

  Dopamine Agonists           Dopamine Antagonists    Dopamine Uptake
                                                      Inhibitors

  Drug Carriers               Dyes                    Emetics

  Emollients                  Endocannabinoids        Endothelium-Dependent
                                                      Relaxing Factors

  Environmental Pollutants    Enzyme Activators       Enzyme Inhibitors

  Estradiol Antagonists       Estrogen Antagonists    Estrogen Receptor
                                                      Modulators

  Estrogens                   Estrogens,              Excipients
                              Non-Steroidal           

  Excitatory Amino Acid       Excitatory Amino Acid   Expectorants
  Agonists                    Antagonists             

  Fat Substitutes             Fertility Agents,       Fertility Agents, Male
                              Female                  

  Fertilizers                 Fibrinolytic Agents     Filaricides

  Fixatives                   Flavoring Agents        Fluorescent Dyes

  Folic Acid Antagonists      Food Additives          Food Coloring Agents

  Food Preservatives          Free Radical Scavengers Fungicides, Industrial

  GABA Agents                 GABA Agonists           GABA Antagonists

  GABA Modulators             Ganglionic Blockers     Ganglionic Stimulants

  Gastrointestinal Agents     Glucocorticoids         Glycine Agents

  Gout Suppressants           Growth Inhibitors       Growth Substances

  GTP Phosphohydrolase        Hallucinogens           Hazardous Substances
  Activators                                          

  Hemagglutinins              Hematinics              Hematologic Agents

  Hemostatics                 Heparin Antagonists     Herbicides

  Histamine Agonists          Histamine Antagonists   Histamine H1
                                                      Antagonists

  Histamine H1 Antagonists,   Histamine H2            HIV Fusion Inhibitors
  Non-Sedating                Antagonists             

  HIV Protease Inhibitors     Hormone Antagonists     Hormones

  Hydroxymethylglutaryl-CoA   Hypnotics and Sedatives Hypoglycemic Agents
  Reductase Inhibitors                                

  Immunosuppressive Agents    Indicators and Reagents Inflammation Mediators

  Insect Repellents           Insecticides            Insulin Antagonists

  Intercalating Agents        Interferon Inducers     Iodophors

  Ionophores                  Iron Chelating Agents   Irritants

  Keratolytic Agents          Leprostatic Agents      Leukotriene Antagonists

  Lipotropic Agents           Lipoxygenase Inhibitors Luminescent Agents

  Luteolytic Agents           Menstruation-Inducing   Miotics
                              Agents                  

  Mitogens                    Molecular Probes        Molluscacides

  Monoamine Oxidase           Mouthwashes             Muscarinic Agonists
  Inhibitors                                          

  Muscarinic Antagonists      Muscle Relaxants,       Mutagens
                              Central                 

  Mydriatics                  Narcotic Antagonists    Narcotics

  Nasal Decongestants         Natriuretic Agents      Neuromuscular Agents

  Neuromuscular Blocking      Neuromuscular           Neuromuscular
  Agents                      Depolarizing Agents     Nondepolarizing Agents

  Neuroprotective Agents      Neurotoxins             Neurotransmitter Agents

  Neurotransmitter Uptake     Nicotinic Agonists      Nicotinic Antagonists
  Inhibitors                                          

  Nitric Oxide Donors         Nootropic Agents        Nucleic Acid Synthesis
                                                      Inhibitors

  Ointment Bases              Oligonucleotides,       Ophthalmic Solutions
                              Antisense               

  Oxidants                    Oxidants, Photochemical Oxytocics

  Parasympatholytics          Parasympathomimetics    Peroxisome
                                                      Proliferators

  Pesticide Synergists        Pesticides              Pharmaceutic Aids

  Pheromones                  Phosphodiesterase       Photoaffinity Labels
                              Inhibitors              

  Photosensitizing Agents     Phytoestrogens          Plant Growth Regulators

  Plasma Substitutes          Plasminogen Activators  Platelet Aggregation
                                                      Inhibitors

  Poisons                     Potassium Channel       Preservatives,
                              Blockers                Pharmaceutical

  Prodrugs                    Progestins              Prostaglandin
                                                      Antagonists

  Protease Inhibitors         Protective Agents       Protein Kinase
                                                      Inhibitors

  Protein Synthesis           Psychotropic Drugs      Pulmonary Surfactants
  Inhibitors                                          

  Pyrogens                    Radiation-Protective    Radiation-Sensitizing
                              Agents                  Agents

  Radiopharmaceuticals        Reducing Agents         Renal Agents

  Respiratory System Agents   Reverse Transcriptase   Riot Control Agents,
                              Inhibitors              Chemical

  Rodenticides                Root Canal Irrigants    Schistosomicides

  Sclerosing Solutions        Selective Estrogen      Serine Proteinase
                              Receptor Modulators     Inhibitors

  Serotonin Agents            Serotonin Agonists      Serotonin Antagonists

  Serotonin Uptake Inhibitors Sex Attractants         Sodium Channel Blockers

  Soil Pollutants             Solvents                Spermatocidal Agents

  Sulfhydryl Reagents         Sunscreening Agents     Surface-Active Agents

  Sweetening Agents           Sympatholytics          Sympathomimetics

  Tear Gases                  Teratogens              Tissue Adhesives

  Tocolytic Agents            Toothpaste              Tranquilizing Agents

  Trypanocidal Agents         Trypsin Inhibitors      Uncoupling Agents

  Uricosuric Agents           Vasoconstrictor Agents  Vasodilator Agents

  Vehicles                                            
  --------------------------- ----------------------- -----------------------

# My NCBI

-   Allows users to customize their search experience in PubMed

-   Allows users to save search strategies

-   Allows PubMed to update those saved searches on a schedule of the
    user's choosing and send the results to the user via email

## Setting up a My NCBI account:

![](media/image28.png){width="6.247222222222222in"
height="1.0729166666666667in"}

Click on register and:

![](media/image29.png){width="3.6034722222222224in"
height="4.353472222222222in"}

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8298611111111112in"   **Write down your username and password** as well as the
  height="0.9208333333333333in"}                         answer to the security question. PubMed cannot recover
                                                         accounts for users who have forgotten this information.

  ------------------------------------------------------ ----------------------------------------------------------

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8298611111111112in"   **Watch for the verification email from PubMed. Respond to
  height="0.9208333333333333in"}                         it.** If you do not verify your email address, no
                                                         automatic updates will be sent.

  ------------------------------------------------------ ----------------------------------------------------------

Once the account has been registered, the My NCBI box will change to a
Welcome:

![](media/image30.png){width="1.8229166666666667in"
height="0.4791666666666667in"}

  ----------------------------------- -----------------------------------------------------
  Your My NCBI account is now ready   ![](media/image30.png){width="1.8229166666666667in"
  for customization. Start by         height="0.4791666666666667in"}
  clicking on the My NCBI link:       

  This will take you to your          ![](media/image31.png){width="1.4583333333333333in"
  account's web page. Look for the    height="0.6145833333333334in"}
  logo in the upper left hand corner: 

  On the left hand side of the        ![](media/image32.png){width="1.4479166666666667in"
  screen, you'll see various options: height="2.7708333333333335in"}
  ----------------------------------- -----------------------------------------------------

My NCBI allows you to customize your PubMed searching:

-   [Save searches.]{.underline} Do you have a specific subject that you
    monitor? Set up the search once and then let PubMed email you,
    automatically, new citations that meet your search criteria.

-   [Set filters.]{.underline} Set limits to your searches once and see
    them every time you search PubMed using your My NCBI account. My
    NCBI has over 70 different filters available.

-   [User Preferences.]{.underline} Enter your preferred email address
    once and then, every time you want to email citations from PubMed,
    that email address will appear as the default address. Type once --
    use over and over and over again via My NCBI.

## Setting Filters in My NCBI

1\. Click on Filters on the blue side bar:

![](media/image33.png){width="2.1145833333333335in"
height="1.6666666666666667in"}

2\. Choose which database you want to work in -- Click on PubMed:

![](media/image34.png){width="5.995138888888889in"
height="1.6513888888888888in"}

2\. Choose which database you want to work in -- Click on PubMed:

![](media/image34.png){width="5.995138888888889in"
height="1.6513888888888888in"}

3\. Configure "Quick Picks" by clicking the desired boxes:

![](media/image35.png){width="5.998611111111111in"
height="3.970833333333333in"}

For example, if English and Free Full Text are checked off, whenever you
are signed into your My NCBI account and PubMed is searched, two new
tabs will show up:

> ![](media/image36.png){width="5.996527777777778in"
> height="2.9368055555555554in"}

Here, it is quickly apparent that out of the 85,543 results there are
62,754 in English. See them by clicking on the English tab. There 6,962
items that have free full text available. See that set by clicking on
the free full text tab.

4\. Click on the "Browse" tab in the My NCBI page to find other
available filters:

![](media/image37.png){width="5.997222222222222in"
height="2.9166666666666665in"}

Simply add filters as desired. **NOTE**: Only 5 filters may be active at
any one time.

## LinkOut for Libraries and My NCBI

Many libraries have provided online access to electronic journals for
faculty, staff, and students via LinkOut for Libraries. To see these
easily, set up a filter. Instructions follow for setting up the filter.

> 1\. From the Browse Filters page (graphic above) click on Libraries.
>
> 2\. A new screen will appear. Scroll down to find your library's name
> in the list. Click on the blue hyperlink (the school name, not the
> globe).
>
> Example: Find U Mass Medical School in the list:

![](media/image38.png){width="5.9944444444444445in"
height="1.2916666666666667in"}

> 3\. From the next screen that pops up, click on "Add a result tab..."
> and "Add a link icon..."

![](media/image39.png){width="5.998611111111111in"
height="2.015972222222222in"}

> 4\. Done! The filter has been set. Now, whenever you search PubMed
> after signing into your My NCBI account, this is what you'll see:
>
> \[graphic next page\]

![](media/image40.png){width="5.99375in" height="2.915277777777778in"}

  ----------------------------------------------------- ------------------------------------------------------
  ![](media/image41.png){width="0.8333333333333334in"   In order to *read* the full text, patrons must be
  height="0.9166666666666666in"}                        accessing PubMed through the special LinkOut URL for
                                                        the specified library.

  ----------------------------------------------------- ------------------------------------------------------

Libraries that participate in LinkOut for Libraries may wish to set up a
**Shared My NCBI account** so that the LinkOut Filter for their library
will automatically display anytime someone accesses PubMed via their
special LinkOut URL.

See the *NLM Technical Bulletin* article, "Share My NCBI Account
Settings," for instructions on how to do this.
<http://www.nlm.nih.gov/pubs/techbull/ja05/ja05_share_my_ncbi.html>

Also**, libraries are now able to** **change the wording on their
library's LinkOut filter tab**. See the NLM Technical Bulletin technical
note, "Choosing a Display Name for the Filter Tab in PubMed," at
<http://www.nlm.nih.gov/pubs/techbull/so05/so05_technote.html#10>

## 

**NOTE:** Filter selections may be changed using either the "My
Selections" link or the
![](media/image42.png){width="0.3333333333333333in"
height="0.22916666666666666in"} icon on the PubMed page.

**Saving Searches in My NCBI**

My NCBI will save search *strategies*. This is different from the
Clipboard which saves search results. Once saved, a search strategy may
be set up for automatic updates. Here's the process:

1\. Set up and run your search in PubMed. Then, click on the Save Search
link:

![](media/image43.png){width="6.003472222222222in" height="2.6875in"}

2\. A new window will open:

![](media/image44.png){width="5.998611111111111in"
height="2.1215277777777777in"}

Clicking on OK at this point will save the search and it may be
[manually]{.underline} updated at any time.

3\. Click on Yes for automatic emailed updates of new search results.
Now, set up the schedule:

![](media/image45.png){width="5.99375in" height="4.584722222222222in"}

When finished, click OK.

  ----------------------------------------------------- -------------------------------- ---------------------------
  ![](media/image41.png){width="0.8333333333333334in"   Name the search                  Naming the search will
  height="0.9166666666666666in"}                                                         *not* affect the search
                                                                                         strategy. The name will be
                                                                                         part of the subject line of
                                                                                         the emailed updates.

                                                        Additional Text                  This will appear in the
                                                                                         emailed updates as:
                                                                                         Sender's Message

                                                        Maximum number of items to send  Keep it low! The emailed
                                                                                         update will provide a link
                                                                                         to all results.

                                                        Schedule                         May be changed at any time

                                                        HTML or Text?                    Depends on your email
                                                                                         system. If your system is
                                                                                         text based, change this
                                                                                         setting to text. If
                                                                                         possible, leave it as HTML.
  ----------------------------------------------------- -------------------------------- ---------------------------

**My Saved Searches page**

![](media/image46.png){width="5.992361111111111in"
height="2.1145833333333335in"}

-   Manually update searches using this page. Select a search, then
    click on the What's New for Selected button.

-   See search strategies by mousing over the search name.

-   Click on the search name hyperlink to retrieve *total* search
    results -- this will not affect any scheduled updates, but retrieval
    will not be limited to just new results.

-   See next scheduled update by mousing over entry in the "Last
    Updated" column.

-   See schedule for updates by mousing over the entry in the "Details"
    column.

-   Change the schedule for updating a search by clicking on the entry
    in the "Details" column.

-   Delete a search or searches by checking the box adjacent to a search
    and then clicking on the Delete Selected button.

# 

+---------------+------------------------------------------------------+
| ![](media/im  | Out with the old, in with the new.                   |
| age41.png){wi |                                                      |
| dth="0.833333 | **Saved search strategies can NOT be edited.**       |
| 3333333334in" |                                                      |
| heig          | Delete the old strategy. Plan your new strategy, run |
| ht="0.9166666 | it in PubMed, then save it in My NCBI.               |
| 666666666in"} |                                                      |
+---------------+------------------------------------------------------+

## Preferences in My NCBI

Use Preference in My NCBI to:

-   Change the email address used for the account

-   Change the way the links display in PubMed

-   Turn on (or off) the highlighting feature in PubMed

![](media/image47.png){width="5.998611111111111in"
height="2.8159722222222223in"}

# LinkOut

LinkOut provides links from PubMed and other Entrez databases to a wide
variety of relevant we-accessible online resources including but not
limited to full text.

![](media/image48.png){width="5.992361111111111in" height="2.46875in"}

**Exercises**

[Using My NCBI]{.underline}

1\. A health professional you work with has library privileges both at
the Forsyth Institute and Harvard Medical school. How would you help
them set up a My NCBI account that would show both sets of holdings?

2\. The family of a child with Marfan syndrome makes quarterly trips to
the child's specialist for check-ups. Help them save a search that will
automatically give them updates concerning this syndrome.

4\. A librarian is interested in marketing services to administration in
order to strengthen the presence of the library in a small hospital. How
could this librarian use My NCBI in this instance?

[Using LinkOut:]{.underline}

1\. Locate a clinical synopsis of fatal familial insomnia.

2\. Does the University of Minnesota Bio-Medical Library have access to
the article "Dentist on TV"? If it does, what format is this article
available in?

3\. What is the melting point of warfarin?

4\. Find a Community of Science author profile for Trisha Greenhalgh. In
what year did she receive the Order of the British Empire?

# Searching with Clinical Queries

Clinical Queries, located on the Sidebar, is PubMed's Evidence-Based
Medicine (EBM) filter-set based upon research done by R. Brian Haynes,
MD, PhD at McMaster University. This set consists of the Clinical
Queries filters and the Systematic Reviews subset.

## Clinical Queries

The MeSH definition for Evidence-Based Medicine is:

> The process of systematically finding, appraising, and using
> contemporaneous research findings as the basis for clinical decisions.
> Evidence-based medicine asks questions, finds and appraises the
> relevant data, and harnesses that information for everyday clinical
> practice. Evidence-based medicine follows four steps: \[1\]formulate a
> clear clinical question from a patient\'s problem; \[2\]search the
> literature for relevant clinical articles; \[3\]evaluate (critically
> appraise) the evidence for its validity and usefulness; \[4\]implement
> useful findings in clinical practice. The term \"evidence based
> medicine\" (no hyphen) was coined at McMaster Medical School in Canada
> in the 1980\'s to label this clinical learning strategy, which people
> at the school had been developing for over a decade. (From BMJ
> 1995;310:1122) Year introduced: 1997.

Following this definition, the purpose of these filters is to aid
clinicians (and librarians!) to perform step 2, "search the literature
for relevant clinical articles." To this end, hedges were established,
using the McMaster work to search for contemporaneous research-based
literature.

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8298611111111112in"   A **hedge** or filter is a "permanent," standardized
  height="0.9208333333333333in"}                         search strategy (usually often used) intended to be used
                                                         in combination with other ad hoc searches.

  ------------------------------------------------------ ----------------------------------------------------------

Clinical Queries provides these hedges for five clinical situations:

-   **Therapy**: Treatment of a disease or condition.

-   **Diagnosis**: Determination of the nature of a disease or condition
    or the distinguishing of one disease or condition from another.

-   **Etiology**: (Also known as **Harm**.) Causation of a disease or
    condition.

-   **Prognosis**: Prediction of the probable outcome of a disease based
    on a individual\'s condition and the usual course of the disease as
    seen in similar situations.

-   **Clinical Prediction Guides**: Pertain to the prediction of some
    aspect of a disease or condition and have been advocated as a
    mechanism for enhancing clinical judgment. Clinical prediction
    studies develop or validate rules, guides, indexes, equations,
    scales, scores or models to predict a diagnosis, prognosis, risk
    (etiology), therapeutic response, therapeutic drug level or clinical
    outcome.

Additionally, Clinical Queries provides two emphasis filters:

-   Narrow, specific search

-   Broad, sensitive search

The result of a Clinical Queries filter search is, especially when an
emphasis of Specificity is applied, a substantial decrease in retrieval
set. However, the set is restricted to research-based citations.

**Example:**

A PubMed search on using statins in the treatment of diabetic patients
who have heart disease:

Search PubMed using the terms: statins heart disease diabetes

> Results = 511 hits. Included in those hits are 5 editorials and 6
> letters; additionally, there are hundreds of non-research-based
> articles.

Search Clinical Queries with the terms: statins heart disease diabetes

Therapy

Narrow, specific search

> Results = 76 hits. None are editorials or letters. Most articles are
> research-based. There is an obvious narrowing of retrieval based on
> the "hedge" supplied by Clinical Queries

Tips for using Clinical Queries:

-   Clinical Queries defaults to Therapy and narrow, specific searches.

-   If a narrow, specific search retrieves too few citations, use the
    broad, sensitive emphasis instead.

-   While natural language searches often work best in the Clinical
    Queries interface, MeSH terminology can be used to reduce large
    retrieval sets, for example: "Heart Diseases \[MH\] AND Diabetes
    Mellitus\[MH\]."

-   Remember that the MeSH database contains a Links menu with a
    "Clinical Queries" option. If clicked, this will send a chosen MeSH
    term directly to the Clinical Queries search box.

-   Copy and paste a search from the MeSH database into the Clinical
    Queries search box for more control.

## Systematic Reviews

The Systematic Reviews strategy is intended to retrieve citations
identified as systematic reviews, meta-analyses, reviews of clinical
trials, evidence-based medicine, consensus development conferences,
guidelines, and citations to articles from journals specializing in
review studies of value to clinicians.

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8298611111111112in"   A **systematic review** is "a summary of the medical
  height="0.9208333333333333in"}                         literature that uses explicit methods to perform a
                                                         thorough literature search and critical appraisal of
                                                         individual studies and that uses appropriate statistical
                                                         techniques to combine these valid studies." (Sackett, et
                                                         al, 2000.) **Meta-analyses** are also systematic reviews
                                                         but they use quantitative methods (statistics) to
                                                         summarize results.

  ------------------------------------------------------ ----------------------------------------------------------

Systematic Reviews are a subset of the MEDLINE database (as opposed to a
hedge). Systematic reviews may also be searched by adding
**systematic\[sb\]** to any PubMed search strategy.

**Some Evidence-Based Medicine Resources**

> McKibbon, Ann, Angela Eady, Susan Marks. (1999). *PDQ: Evidence-Based
> Principles and Practice.* Saint Louis: B.C. Decker Inc.
>
> Sackett, David L, Sharon E. Straus, W. Scott Richardson, William
> Rosenberg, R. Brian Haynes. (2000). *Evidence-Based Medicine: How to
> Practice and Teach EBM.* New York: Churchill Livingstone.
>
> McLucus, Katherine. (2003). *A Student's Guide to the Medical
> Literature*. Denver: University of Colorado Health Sciences Center,
> Dennison Memorial Library. Retrieved June 3, 2003 from
> <http://denison.uchsc.edu/SG/> (PDA version available at
> http://denison.uchsc.edu/SG/PDA.html).

There are also numerous websites available with information regarding
EBM:

> Evidence Based Medicine: Tutorial
> <http://www.hsl.unc.edu/services/tutorials/ebm/welcome.htm#top>
>
> Duke University Medical Center Library and Health Sciences Library,
> University of North Carolina at Chapel Hill.
>
> Evidence Based Medicine: Information and tutorial
>
> <http://library.umassmed.edu/EBM/>
>
> Lamar Soutter Library, U Mass Medical School
>
> Centre for Evidence Based Medicine (CEBM)
>
> <http://www.cebm.net/index.asp>

[]{#__RefHeading___Toc119233570 .anchor}**Medical Genetics Searches**

Again, this provides a set of hedges or filters aimed at narrowing
retrieval. The hedges were developed in conjunction with the staff of
GeneReviews: Genetic Disease Online Reviews at GeneTests, University of
Washington, Seattle.

![](media/image49.png){width="4.697222222222222in"
height="2.2604166666666665in"}

Please note that the default is to have **all** the listed categories
checked. It may be useful to turn off the default and simply select the
categories that may be most relevant to your search.

# Creating Web Links to PubMed 

The Entrez system allows for the creation of URL links that search and
retrieve documents from PubMed in three ways:

1.  **Entrez Utilities** -- These are generally used by researchers who
    are primarily looking to pull large amounts of sequence data from
    NCBI databases. See
    <http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html>
    for more information. NLM also offers classes in this sort of
    scripting

2.  The **URL button** on the details screen -- which saves a particular
    search strategy as a specific URL and will, on command, execute that
    specific PubMed search

3.  **Manually constructed URLs**.

Manually created URL links may be stored on a library website.

-   Want to put a section on your library's website that says, "Click
    here for current information on avian flu"? Writing a manual link to
    PubMed can allow you to do that.

-   Want to put a section on your library's web page that says "PubMed
    articles by our faculty"? Writing a manual link to PubMed can allow
    you to do just that.

-   These links can be use for finding every article on a given topic,
    through a date range, or for creating current awareness searches
    that find articles published in a given number of past days.

+-------------+--------------------------------------------------------+
| ![](med     | Complete instructions for writing web links to PubMed  |
| ia/image41. | can be found at                                        |
| png){width= |                                                        |
| "0.83333333 | <http://                                               |
| 33333334in" | www.ncbi.nlm.nih.gov/entrez/query/static/linking.html> |
| height="    |                                                        |
| 0.916666666 |                                                        |
| 6666666in"} |                                                        |
+-------------+--------------------------------------------------------+

Begin a URL with the NCBI address, a search command, and a choice of
database:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=**Command**&db=**Database**&...\
\
For our purposes, **Command** is Search and **Database** is PubMed. For
example, this is the beginning of a PubMed search query:\
\
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=**search**&db=**pubmed**&...

\[A variety of search commands for use with PubMed in conjunction with
Entrez's molecular biology databases exist but are beyond the scope of
this lesson; for more information go to
<http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html>.\]

  ------------------------------------------------------ ----------------------------------------------------------
  ![](media/image10.jpeg){width="0.8298611111111112in"   Spaces within a URL cause problems for many web browsers.
  height="0.9208333333333333in"}                         Convert them to "+" signs, for example, Helv Chim Acta
                                                         becomes Helv+Chim+Acta.

  ------------------------------------------------------ ----------------------------------------------------------

To specify search strategies, display formats, and date range, other
pieces of syntax, may be added to the URL. Of special interest are
**Term**, **Doptcmdl**, and the **Pmfilter** family.

## 

## Searching

**Term** permits the addition of search terms such as MeSH terms,
subheadings, natural language terms, and field tags. Nesting of searches
may also be done using **Term**. The syntax for **term** is:\
\
**&term=\
\
**Example:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed**&term=**

-   Use **&term** to perform simple searches:\
    **&term**=food+hypersensitivity

-   Field tags may also be used:\
    **&term**=food+hypersensitivity\[mh\]+AND+2002\[pdat\]\
    \
    **&term=**food+hypersensitivity\[mh\]+AND+cam\[sb\] (this limited
    the search to the Complimentary Medicine Subset)

-   Nesting is similar to nesting done in the PubMed search box:\
    **&term**=(bronchitis+OR+asthma)+AND+(drug+therapy+OR+diet+therapy)

-   Phrase searching may be forced, by using a combination of double
    quote marks and + signs:\
    **&term**="food+hypersensitivity"

## Formats

**Doptcmdl** lets the searcher determine the PubMed format of the
search. The syntax of the search is:\
\
**&doptcmdl=*format***\
\
where format is one of the following for PubMed (see Entrez Help for
information on other Entrez databases):

  ----------------- ----------------- ----------------- ----------------------
  DocSum            Brief             Abstract          Citation

  MEDLINE           XML               ASN.1[^1]         ExternalLink[^2]^\*^
  ----------------- ----------------- ----------------- ----------------------

**Example**:

To search for articles on Coronary Artery Bypass in MEDLINE format use
the following syntax:\
\
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed\
&term=food+hypersensitivity&**doptcmdl=**medline

## 

## Date Ranges

**Pmfilter** is the family of filters used to limit a search between two
dates. The dates can be fixed or relative.

**Fixed Dates\
**Use this sequence of commands to limit a search between two specific
dates.

-   cmd=**Search**

-   term=food+hypersensitivity \[search strategy\]

-   db=**pubmed** \[database choice\]

-   orig_db=**pubmed** \[=database choice above\]

-   pmfilter_DateRange_Field=**Publication**+date \[determines the kind
    of date filtering to be done\]

-   filters=on \[turns filtering on\]

-   pmfilter_DateRange_MinYear=YYYY \[year of beginning date\]

-   pmfilter_DateRange_MinMonth=MM \[month of beginning date\]

-   pmfilter_DateRange_MinDay=DD \[day of beginning date\]

-   pmfilter_DateRange_MaxYear=YYYY \[year of termination date\]

-   pmfilter_DateRange_MaxMonth=MM \[month of termination date\]

-   pmfilter_DateRange_MaxDay=DD \[day of termination date\]

**Example:**

To search PubMed for citations on the MeSH term food hypersensitivity
from 200/01/30 to 2001/12/01 enter:\
\
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?\
cmd=search&db=pubmed&orig_db=PubMed&term=food+hypersensitivity\[mh\]\
**&filters**=on&**pmfilter_DateRange_Field**=Publication+Date\
**&pmfilter_DateRange_MinYear**=2000**&pmfilter_DateRange_MinMonth**=01\
**&pmfilter_DateRange_MinDay**=30\
**&pmfilter_DateRange_MaxYear**=2001**&pmfilter_DateRange_MaxMonth**=12\
**&pmfilter_DateRange_MaxDay**=01

## Relative Dates

Use these relative date filters to limit a search for citations whose
dates fall between a number of days ago and today\'s date.

-   cmd=**Search**

-   term=hay+fever

-   db=**pubmed**

-   orig_db=**pubmed**

-   pmfilter\_**X**DatLimit=NNN+\[Days/Years\], where X is one of the
    following (**X** is case sensitive):

    -   E - entrez (PubMed) \[to base the query upon the Entrez
        date---the date the article was added to the database, not the
        same as the date of publication\]

    -   P - Date of Publication (PubMed)

**Example:**\
\
To search for PubMed citations on food hypersensitivity published within
the last 90 days:

cmd=search&term=coronary+artery+bypass&db=PubMed&orig_db=PubMed\
&**filters=on**&**pmfilter_EDatLimit**=90+Days

##  

**[N]{.underline} [O]{.underline} [T]{.underline} [E]{.underline}
[S]{.underline}**

**[N]{.underline} [O]{.underline} [T]{.underline} [E]{.underline}
[S]{.underline}**

[^1]: ^^ *Abstract Syntax Notation number One* is a formal notation
    used for describing data transmitted by telecommunications protocols

[^2]: ^\*\*^ This format is for LinkOut links.