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!
MeSH for pharmacists
Using MeSH in PubMed for pharmacists Martin Morris / email@example.com
It can be hard to keep up… but PubMed can help…!
OverviewIn this short presentation we will be looking atsome Search Builder features of PubMed and howthey 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.
First things first… How can MeSH and search tags help pharmacists to create more focused PubMed searches?
Finding PubMed and MeSHWe will be focusing on two partsof the PubMed system. Thesecan be accessed from thePubMed front screen.PubMed is where we canretrieve citations of interest bythe use of relevant search terms.MeSH is the part of PubMedwhere we can find specificMedical Subject Headings.Pharmacists will also beinterested in other databasessuch as PubChem, howeverthese are beyond the scope ofthis brief presentation.
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.
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.
Not all substances are MeSH terms…Not all substances have their ownMeSH heading. An example ispholcodine, on the right. This is aSupplementary 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.
Let’s look at an exampleWhen searching for substance-related citations in PubMed, there aretwo search tags which can be used to specify either a substance with aMeSH heading, or a supplementary concept. These are [mh] (MeshHeading) and [nm] (Substance Name). Let’s see how they can help.A search for just pholcodine. We A search for pholcodine[nm] giveshave 77 results where pholcodine 33 results where the citation hasoccurs anywhere in the citation. been MeSH tagged: pholcodine.
Continuing with pholcodine[nm]This is the first citation fromthe pholcodine[nm] search.We can see that pholcodineis one of the Substances tagsassigned to this citation.This is the case for all 33results of our search.NOTE: The [nm] search tagwill find both chemicalswhich are full MeSH entries,or those which areSupplementary Concepts.The [mh] tag will onlyretrieve full MeSH entriesand should therefore beused with some care.
Let’s tackle a real question! Have there been any recent papers on the use of aspirin as a cyclooxygenase inhibitor to treat thrombocytosis?
Performing the search without tagsUsing the search expression aspirin thrombocytosis cyclooxygenaseinhibitor gives us 224 results. This is manageable but there are somecitations that look less relevant. We can also see in the Search detailsthat PubMed has translated our expression in a broad way.
Repeating with Search Builder/MeSHSearch Builder is a PubMed tool which can help us to select the rightMeSH terms with appropriate search tags.In addition to using the [mh] or [nm] search tags, we can also pull inpharmacologic 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.
Building the search: aspirinFrom the PubMed front screen,select MeSH and search for theentry for aspirin.We can now add this to thesearch builder with the Add tosearch builder button. We couldalso use one of the subheadings:the therapeutic use subheadingwould be appropriate.Clicking the Add to searchbuilder button gives us a [Mesh]tagged and precise search term.
Adding cyclooxygenase inhibitorThis is a pharmacological action.As appropriate pharmacologicalactions are listed for eachsubstance, we can go to this partof the entry and select the onewe require.Selecting cyclooxygenaseinhibitors returns the appropriateMeSH entry, along with a list of allsubstances associated with thisaction. Clicking the Add to searchbuilder button shows that we nowhave a [Pharmacological Action]search tag added.
Adding thrombocytosisAs for aspirin, we search forthrombocytosis in MeSH. Wenote that two subheadings:therapy and drug therapy,appear appropriate andtherefore select them.The search will retrieverelevant thrombocytosiscitations which deal withEITHER therapy OR drugtherapy of the condition. Oursearch is now ready to run sowe click on Search PubMed.
A more focused set of resultsWe now have a reducedand more focused set of154 results.Search Builder hashelped us to build atargeted search throughthe use of controlledvocabulary and theaddition of relevantsearch tags such as[mh], [nm] and [pa].We shall now take a lookat a final way ofretrieving specific typesof study: ClinicalQueries and SystematicReviews.
Some final tips for pharmacists Can MeSH, search tags and the Search Builder help me find Clinical Queries and Systematic Reviews?
Clinical Queries, Systematic ReviewsPubMed has powerful filterswhich can retrieve citationsdealing with clinical queriesat the point of care, orsystematic reviews ofclinical trials and evidencebased medicine. These arevery useful to pharmacists.HOWEVER: the searchbox provided in this sectionis basic and doesn’tprovide access to theSearch Builder.Is there a way of gettingaround this problem?
Clinical Queries, Systematic ReviewsThere are several ways, but we will brieflyintroduce 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.
The subset [sb] search tagThe second way involves our final search tag: [sb].This stands for subset and allows us to select a predefined subset ofcitations directly from the search line.PubMed has defined a number of different subsets, the mostrelevant to pharmacists are: cam[sb] Complimentary Medicine cancer[sb] Cancer dietsuppl[sb] Dietary Supplements systematic[sb] Systematic Reviews tox[sb] Toxicology
The subset [sb] search tag #2The [sb] tag is easy to use. We simply add relevant subset to the end ofour 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 tothis search string.("Aspirin/therapeutic use"[Mesh] AND"Cyclooxygenase Inhibitors"[Pharmacological Action])AND ("Thrombocytosis/drug therapy"[Mesh] OR"Thrombocytosis/therapy"[Mesh]) AND systematic[sb]
The subset [sb] search tag #3And we find that our number of results has been reduced to 2! Both ofthese are systematic reviews of the use of aspirin as a cyclooxygenaseinhibitor in the treatment of thrombocytosis.
Pitfalls to watch out for Is there anything I need to watch out for when using MeSH and search tags in my searches?
Pitfalls to watch out for1. 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.
Questions Thank you for your attention. Do you have any questions?