Unit 3 Emotional Intelligence and Spiritual Intelligence.pdf
MeSH for pharmacists
1. Using MeSH in PubMed
for pharmacists
Martin Morris / aaa@bb.com
2. It can be hard to keep up…
but PubMed
can help…!
3. Overview
In this short presentation we will be looking at
some Search Builder features of PubMed and how
they can help pharmacists to find information.
We will:
• Look at some of the features of PubMed of most
interest to pharmacists.
• See some tips on how to find chemicals and drugs,
meet MeSH and see the power of search tags.
• Through a worked example, learn how MeSH and
search tags can focus our searches.
• Discover some pitfalls to watch out for.
4. First things first…
How can MeSH and
search tags help
pharmacists to
create more focused
PubMed searches?
5. Finding PubMed and MeSH
We will be focusing on two parts
of the PubMed system. These
can be accessed from the
PubMed front screen.
PubMed is where we can
retrieve citations of interest by
the use of relevant search terms.
MeSH is the part of PubMed
where we can find specific
Medical Subject Headings.
Pharmacists will also be
interested in other databases
such as PubChem, however
these are beyond the scope of
this brief presentation.
6. A quick MeSH refresher
Meet MeSH…
• MeSH stands for Medical
Subject Headings. It is the
controlled vocabulary used
within PubMed.
• Citations within PubMed are
assigned MeSH headings to
make them easier to find.
• MeSH has an entire section
devoted to roughly 180,000
chemicals and drugs. An
example is on the left.
• MeSH terms usually have
Subheadings assigned to them.
If using a MeSH term in a
search, these allow us to make
our search even more precise.
7. A quick MeSH refresher cont’d…
What else is there in
a MeSH heading?
• In addition to the above, a MeSH entry for
a substance also gives a list of synonyms,
brand names etc.
• A MeSH search against any of these will (in
this example) bring up the entry for
methadone. As drugs often have many
names, this can be very helpful.
• Note the Pharmacologic Actions. These are
controlled terms which describe the actions of
the substance – we shall return to these later.
Methadone has three Pharmacologic Actions.
• Finally, notice how methadone fits into
the MeSH hierarchy. We can see that
MeSH has an entire branch dedicated to
Chemicals and Drugs.
8. Not all substances are MeSH terms…
Not all substances have their own
MeSH heading. An example is
pholcodine, on the right. This is a
Supplementary Concept.
• This may be because the substance
has only recently entered the
literature. This will be considered
at the next MeSH update.
• Sometimes it is felt by chemists at
PubMed that it isn’t a new concept
– for example, we can see that the • Note the Entry Term 7,8-
pholcodine heading was didehydro-4,5 alpha-epoxy-17-
introduced in 1974. This methyl-3-(2-morpholino-
substance’s heading is mapped to ethoxymorphinan-6 alpha-ol).
Codeine/analogs and derivates or • Substances in MeSH are indexed
Morpholines in MeSH. by their common name.
9. Let’s look at an example
When searching for substance-related citations in PubMed, there are
two search tags which can be used to specify either a substance with a
MeSH heading, or a supplementary concept. These are [mh] (Mesh
Heading) and [nm] (Substance Name). Let’s see how they can help.
A search for just pholcodine. We A search for pholcodine[nm] gives
have 77 results where pholcodine 33 results where the citation has
occurs anywhere in the citation. been MeSH tagged: pholcodine.
10. Continuing with pholcodine[nm]
This is the first citation from
the pholcodine[nm] search.
We can see that pholcodine
is one of the Substances tags
assigned to this citation.
This is the case for all 33
results of our search.
NOTE: The [nm] search tag
will find both chemicals
which are full MeSH entries,
or those which are
Supplementary Concepts.
The [mh] tag will only
retrieve full MeSH entries
and should therefore be
used with some care.
11. Let’s tackle a real question!
Have there been any
recent papers on the
use of aspirin as a
cyclooxygenase
inhibitor to treat
thrombocytosis?
12. Performing the search without tags
Using the search expression aspirin thrombocytosis cyclooxygenase
inhibitor gives us 224 results. This is manageable but there are some
citations that look less relevant. We can also see in the Search details
that PubMed has translated our expression in a broad way.
13. Repeating with Search Builder/MeSH
Search Builder is a PubMed tool which can help us to select the right
MeSH terms with appropriate search tags.
In addition to using the [mh] or [nm] search tags, we can also pull in
pharmacologic actions in a way that doesn’t involve error-prone typing.
[nm] aspirin
[MeSH] thrombocytosis
*[Pharmacologic Action] cyclooxygenase
inhibitor
*For future reference, this is equivalent to the [pa] search tag.
14. Building the search: aspirin
From the PubMed front screen,
select MeSH and search for the
entry for aspirin.
We can now add this to the
search builder with the Add to
search builder button. We could
also use one of the subheadings:
the therapeutic use subheading
would be appropriate.
Clicking the Add to search
builder button gives us a [Mesh]
tagged and precise search term.
15. Adding cyclooxygenase inhibitor
This is a pharmacological action.
As appropriate pharmacological
actions are listed for each
substance, we can go to this part
of the entry and select the one
we require.
Selecting cyclooxygenase
inhibitors returns the appropriate
MeSH entry, along with a list of all
substances associated with this
action. Clicking the Add to search
builder button shows that we now
have a [Pharmacological Action]
search tag added.
16. Adding thrombocytosis
As for aspirin, we search for
thrombocytosis in MeSH. We
note that two subheadings:
therapy and drug therapy,
appear appropriate and
therefore select them.
The search will retrieve
relevant thrombocytosis
citations which deal with
EITHER therapy OR drug
therapy of the condition. Our
search is now ready to run so
we click on Search PubMed.
17. A more focused set of results
We now have a reduced
and more focused set of
154 results.
Search Builder has
helped us to build a
targeted search through
the use of controlled
vocabulary and the
addition of relevant
search tags such as
[mh], [nm] and [pa].
We shall now take a look
at a final way of
retrieving specific types
of study: Clinical
Queries and Systematic
Reviews.
18. Some final tips for pharmacists
Can MeSH, search
tags and the Search
Builder help me find
Clinical Queries and
Systematic Reviews?
19. Clinical Queries, Systematic Reviews
PubMed has powerful filters
which can retrieve citations
dealing with clinical queries
at the point of care, or
systematic reviews of
clinical trials and evidence
based medicine. These are
very useful to pharmacists.
HOWEVER: the search
box provided in this section
is basic and doesn’t
provide access to the
Search Builder.
Is there a way of getting
around this problem?
20. Clinical Queries, Systematic Reviews
There are several ways, but we will briefly
introduce the two most relevant.
1. Taking another look at our set of
results, we see a link to Clinical
Queries results. The top results are
already shown, with a link to Try
Clinical Queries.
Selecting this link takes us to the
Clinical Queries page, with our
full query copied into the
simpler search box.
This provides instant access
to Clinical Studies,
Systematic Reviews and
Medical Genetics citations.
21. The subset [sb] search tag
The second way involves our final search tag: [sb].
This stands for subset and allows us to select a predefined subset of
citations directly from the search line.
PubMed has defined a number of different subsets, the most
relevant to pharmacists are:
cam[sb] Complimentary Medicine
cancer[sb] Cancer
dietsuppl[sb] Dietary Supplements
systematic[sb] Systematic Reviews
tox[sb] Toxicology
22. The subset [sb] search tag #2
The [sb] tag is easy to use. We simply add relevant subset to the end of
our query string. For our previous example…
("Aspirin/therapeutic use"[Mesh] AND
"Cyclooxygenase Inhibitors"[Pharmacological Action])
AND ("Thrombocytosis/drug therapy"[Mesh] OR
"Thrombocytosis/therapy"[Mesh])
…we add AND systematic[sb] to retrieve Systematic Reviews related to
this search string.
("Aspirin/therapeutic use"[Mesh] AND
"Cyclooxygenase Inhibitors"[Pharmacological Action])
AND ("Thrombocytosis/drug therapy"[Mesh] OR
"Thrombocytosis/therapy"[Mesh]) AND systematic[sb]
23. The subset [sb] search tag #3
And we find that our number of results has been reduced to 2! Both of
these are systematic reviews of the use of aspirin as a cyclooxygenase
inhibitor in the treatment of thrombocytosis.
24. Pitfalls to watch out for
Is there anything I
need to watch out
for when using
MeSH and search
tags in my searches?
25. Pitfalls to watch out for
1. Pharmacological Action terms have
only been in use since 1996.
2. Some MeSH substance headings
have been in use longer than others.
The date of introduction can be
checked when searching a MeSH
heading for a substance.
3. Citations do not arrive in PubMed
with MeSH headings already added.
Zidovudine (an HIV medication), is
continues to generate much
research – some of these citations
are very recent, are yet to be
indexed and would therefore be
missed through a pure MeSH-led
search strategy.
26. Questions
Thank you for
your attention.
Do you have any
questions?
Notes de l'éditeur
Today I’d like to take a brief look at how MeSH can help pharmacists to create focused searches in PubMed. In particular, I’m going to explain what a search tag is, and how certain search tags may be of particular interest to pharmacists in their searching. It’s only a brief introduction so I won’t be able to take this too far but I will give an overview which I think would prove useful to pharmacists doing searches.
Things change constantly in pharmacy. New drugs appear, or change names, new uses are found, and it can be rather hard. It’s such a well known phenomenon that there are even cartoons about it! (click to reveal).
This slide rather speaks for itself.
So, our first question… (read question)
Before going any further, I think it might be useful to have a brief of where to find PubMed and MeSH from the main screen. (then do reveals) If we select the drop-down box from the main PubMed screen we see something like this… Stress: PubMed is where actual citation searches are carried out. MeSH is where the subject heading directory is kept.
Explain that we have got to this screen by selecting MeSH from the main screen.We have got to this screen by searching for methadone in the MeSH box.This is a substance with a full MeSH heading, shortly we will look at [Supplementary Concept], formerly [Substance Name]Strongly emphasise the subheadings, as we’re going to use those in the aspirin example later on.Lead into next slide by pointing out that this isn’t the full screen and that the entry has further information.
This is a view of the bottom part of the methadone screen.
Substances which don’t have their own MeSH heading are known as a [Supplementary Concept], or sometimes as a [Substance Name].Substances in MeSH are indexed by their common name, not the IUPAC name, but a IUPAC search will find the substance. This search can sometimes be rather tricky – but point out that it is possible to search by part of the IUPAC name to get a listing – this is beyond the scope of today’s presentation.
Now that we have refreshed our memory of MeSH, we will look at search tags.Say what a search tag is at this stage – a small term in [ ] square brackets that specifies where in the citation we should be searching.For the 77 results – emphasise thatpholcodine appears anywhere in the citation because it hasn’t been tagged in the search. We can see that in the Search Details box.This could be just as a mention in passing somewhere deep in the main text. The [nm] search tag tells PubMed that we only want citations which have been specifically tagged by a MeSH indexer as a relevant substance – hence the narrower search in the Search Details box.Point out that [Supplementary Concept] appears to be the newer version of [Substance Name] = [nm] - the Search Details box prefers to spell it out with longer versions.
Emphasise that we have used the MeSH database to find the right terms, and then used these in our search to get targeted citations. This is the beauty of knowing a few simple search tags.
Speaks for itself.
We have seen how performing searches without search tags can lead to a larger number of possibly less relevant citations. Here, point out the many aspects of the full search detailed view (Search Details) such as “aspirin”[MeSH Terms] OR “aspirin”[All Fields] which is very broad. The same goes for other parts of the search expression. We also just see cyclooxygenase as a single search term. PubMed has done its best to translate out search, but we would welcome a way that would save us some time (as pharmacists are busy people) and ensure that we have focused results.Point out no.4 as one example of a less relevant search result. There are others where the main focus is on another drug and where aspirin is mentioned in less detail.
So we’re going to introduce a tool which called Search Builder and see how it makes use of suitable search tags and controlled vocabulary to create very sharp searches.We can already see from what we have learned that different parts of our clinical query natural relate to certain search tags. Here is now… (reveal)
Second part – “Remember those subheadings we saw earlier in our MeSH search for aspirin? It’s beyond the scope of this presentation to go into all of these in detail, but it’s useful to see how they can sharpen our search.”Third part – “We can see how the /therapeutic use term has been added to our search. If we were typing directly into the PubMed search box we may well not have thought about this addition unless we were very experienced with PubMed.”
We are finding cyclooxygenase inhibitor in the aspirinMeSH screen, we have not had to do a separate search, it’s all laid on for us. However, we can also do a separate MeSH search if we wish (for example to find out more info about the term before adding it to our search).Note that the AND is in capitals. If using these search techniques directly on the search line, the Boolean operators must be in CAPITALS in PubMed to be interpreted properly. If we use search builder, this is done for us.
Note that Search Builder is continuing to add relevant search tags for us.
Note that we can go further and refine our search using Limits or with other search tags (such as limiting results to studies concerning humans rather than animals, or published in the last X years). Again, this is beyond the scope of our brief presentation.
So we’ve now seen the Search Builder, MeSH and its controlled vocabulary, some search tags such as [nm] and [pa], and how those helped us to produce a focused search. What if we are too busy to go through 154 citations (certainly a possibility for a pharmacist!) and would like only those results which will quickly help us to make clinical decisions? In other words… (read question)
Explain briefly how to get to the Clinical Queries bit.Make an aside that the searcher might want to consult some of the EBP resources from muhclibraries.mcgill.ca – such as Cochrane.HINT: the answer is YES
Emphasise the complex search expression copied into the box.
Remember that the AND has to be in capitals, as we said earlier.
That comes to the end of our brief intro to MeSH, search tags and the Search Builder. But before I conclude I’d like to very briefly touch on some pitfalls to be aware of when using this method for searching.
Searches for citations prior to this will result in no hits. In these cases it may be necessary to resort to full text searches, title words, or untagged search terms.Remember pholcodine being introduced in 1974? If you find that your term was only introduced relatively recently, check out what the previous index term was, this is included in the MeSH heading. You might want to run two separate searches, one for each index term, to ensure you get a complete list of hits.Briefly explain what PubMed – In Process and PubMed – as supplied by publisher mean. For this example, you may wish to run a simpler non-MeSH search.A further alternative exists for each of these problems – ask a librarian who will be pleased to help!