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PubMed and other Online Tools
Michele R. Tennant, Ph.D., M.L.I.S.
Health Science Center Libraries
GMS 6014
[email protected]
January 2016
HSCL Sessions
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Searching tips
Entrez
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PubMed – journal literature
OMIM – review articles
Nucleotides, Proteins, RefSeq – sequence databases
Gene – gene-centered information hub
Taxonomy Browser – taxon-centered information hub
Effective Searchers ...
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know the content of the database
• subjects, data types, years of coverage, curated
vs. non-curated
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understand the structure of the database
• record structure, searchable fields, controlled vs
non-controlled vocabularies, search keys
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understand searching options and tools
• thesaurus, limits, preview/index, AND/OR,
related records, etc.
Entrez
Entrez
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Search tool on the NCBI website
Contains a variety of databases:
• Nucleotide sequence; Protein sequence;
Molecular structure; SNPs; Expression
data; Journal literature
• Each “database” contains “records”
• Each “record” in database contains “fields”
Entrez Search Options
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Similar among the various databases
• Entrez conventions: AND, OR, NOT, *
• Three ways to search:
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Basic: just enter your search terms
Advanced: more controlled search - uses limits,
preview/index, history
Complex Boolean: command language with
qualifiers in brackets;
• syntax= term [field] AND term [field] etc.
Entrez Differences
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Differences among the various
databases
• Different search fields available
• Different limits available
• Some controlled, some non-controlled
• Some archival, some curated
PubMed
PubMed
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Journal literature database
“Indexed” from 1946 on (but includes older nonindexed articles)
Over 23 million records; almost 6,000 journals
International in scope and language
Pre-clinical and clinical information
Most citations include abstract
Takes advantage of controlled vocabulary search
(better than keyword alone)
Multiple subsets - MEDLINE, In Process, Publishersupplied
Two Ways to Get to PubMed
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Directly at http://www.ncbi.nlm.nih.gov/sites/entrez?db=
PubMed
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Through HSC Library’s webpage
(recommended):
• http://www.library.health.ufl.edu/
• Click on “Find” then “Databases” then
“PubMed”
Controlled vs Non-controlled
Vocabularies
• “Old People” Example
Controlled Vocabulary
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Controlled terms act as “umbrella” to pick up
all synonyms, spelling differences
(hemoglobin/haemoglobin), singular vs plural,
etc.
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In PubMed, use MeSH Database to find and
search controlled MeSH terms (Medical Subject
Headings)
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Once in MeSH Database, can use additional
options to enhance search (major heading,
subheadings, etc.)
MeSH Example
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Find journal articles on the “physiology
of membrane channels in mitochodria”
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Try the search again so that you discard
peripheral articles.
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Search PubMed
Enter PubMed through our direct
link (rather than through NCBI)
and you will be able to directly
see if the HSCL owns the journal
articles you find
The “ufhsclib” indicates
that you have entered
PubMed correctly, and
that the journals the
library owns will be
apparent
Use the MeSH Database
as a dictionary to find
the appropriate MeSH
term, and then to refine
your search
Note that we have left PubMed and are in
the MeSH “dictionary”
You typed “membrane
channels” into MeSH
database
This tells you to use “ion
channels” rather than
membrane channels
Topical subheadings
help focus search to
one or more aspects
of the subject
Check here and your topics will be the main point of
the articles you find – you won’t get peripheral
citations. Not recommended the first time you search
a topic – if there are few papers in existence for your
topic, you may be left with no articles at all
If you searched on any of these
terms in MeSH, you would be led
to the MeSH term “ion channels”
Note that the
term “ion
channels” will
pick up all the
more specific
types of ion
channels
1. Add your search to
the Search Builder
2. MeSH then automatically builds the
search for you – in this example, you are
looking for papers in which the
physiological aspects of ion channels are
the main point of all the articles you
retrieve
3. Click “Search PubMed”
Once you have added the search
to the Search Builder, and clicked
on “Search PubMed”, you leave
the MeSH Database, and the
search is performed in PubMed
Note that this is the search the MeSH Database built for you – it used the
MesH term “ion channels”, glued “physiology” directly to the search by using
the slash, and picked up all the different types of ion channels. MeSH also
retrieved only the papers where these topics were the main points of the
articles. You did not need to do any of this yourself – MeSH did it for you
once you found the proper MeSH term, and clicked on subheading. Now we
need to complete the second half of the search – mitochondria
Now we need to complete the
second half of the search –
mitochondria. Pull down the
drop-down so you are in MeSH
again, and search for the MeSH
term. Look through the list to
see if there is one that is most
appropriate. Since we did not
specify which type of
mitochondria, we can choose
the general term “mitochondria”.
Read the “scope note” to be
sure which term to choose.
Scope Note
As in the membrane channel
search, you can choose a
subheading and limit to articles
where this topic is the main point;
I’ve chosen not to do so here, as
the search did not specify it (if you
don’t choose subheadings or main
point, remember to click on the
check box next to “mitochondria”).
Send to search box; click “search
PubMed”
You’ve now found articles on
mitochondria, but you need to
combine the ion channel with
mitochondria concepts
Boolean Operators
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Search statements may be combined
using AND, OR, NOT
AND
OR
NOT
To combine searches, choose “Advanced Search”
The Advanced
Search screen
displays your
PubMed history;
from here you can
combine your two
searches using the
appropriate
Boolean operator
Click to
broaden
search
Results of our combined search. You
have now found papers in which the
physiology of membrane channels is the
main point of the article. Each of those
papers is also about mitochondria.
MeSH etc.
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MeSH Database:
• Found appropriate search terms
• Automatically exploded “mitochondria”, so narrower
terms (“mitochondria, muscle”, “mitochondria,
heart”, etc) were ORed together
• Allowed the addition of subheadings (physiology) to
narrow to a particular aspect
• Allowed narrowing to “main point” (throw away
peripherals)
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Use History to combine (AND)
MeSH Caveats
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Performing a MeSH search is usually more precise and
exhaustive than a keyword search, however:
• The most recent papers are not searched - therefore
should also complete a keyword search “in process”
• Very new concepts/scientific terms may not yet be
represented by MeSH
• Very specific or rare concepts may never be represented
by MeSH
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So sometimes you will need to do a keyword search as well
Most Current Articles
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To find the most recent papers – can’t use MeSH
Must perform a keyword search
• OR together synonyms, singular/plural, spelling
variations
• Use * for truncation
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Don’t re-search the entire database – just the parts
without MeSH:
• NOT Medline [sb]
Link Out to E-journals
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Remember, if you entered PubMed directly from the HSCL’s
icon, you can see if the HSCL owns the journal articles you
found
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Choose the “abstract” or “citation” displays from the
pulldown menu
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Blue icons tell if the HSCL owns that journal issue in print;
journal logos or “Find it at UF” lead to online access
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Will NOT tell you what is available in print at other campus
libraries
Summary
Change display settings
to “abstract” view to see
journal icons
Click to broaden
search
Journal links
Similar articles
OMIM - Online Mendelian
Inheritance in Man
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http://www.omim.org/
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Catalog of human genes and genetic disorders
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23,305 records (as of 1/12/16)
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Records are basically “review articles”
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Records link to PubMed, sequences, structures, etc.
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Search tips:
• Look for your disease in “title” field on from advanced search
• If your disorder is listed as a phrase, put phrase in quotation marks
Choose the “Advanced
Search” option for “OMIM”
We will search for information on
“lmna”, but first we limit so that we
search only in the title field
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Limit so that
your term(s)
reside only in
the “title”
This is a phenotype (trait, disease, disorder) record
The other two records are gene
records, and provide primary
information on genes and
proteins.
Official OMIM Number
Table of Contents for
this disorder
Official OMIM Title
You can often easily see
which gene when mutated
causes the disorder
Click on the OMIM #150330 from
the text of the phenotype record,
and you end up at the gene record
Note that if the name of your
disorder is a phrase, you will
need to use quotation marks
in your advanced search