Chapter 5

Medical
databases

Rhanderson Cardoso, MD

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 Chapter 5 - Medical databases

Let’s recap our steps up to this point.

You had an idea for a research project based on one of the methods described in the
first class.
You set your idea according to the PICOTT format and established inclusion/exclusion
criteria.
You confirmed the viability of your idea.
Finally, in the last class, you developed a search strategy focused on PubMed.
Perfect! The next step is taking your search strategy beyond PubMed. It is expected of a
systematic review and meta-analysis to run the search in, at least, three different medical
databases. The goal, remember, is to find all the studies that fit our inclusion criteria.
Each medical database has its singularities and mechanisms for advanced search. However,
in my opinion, those advanced strategies, specific to each platform, add unnecessary
complexity with questionable added value.
Thus, my recommendation is to simplify. Use the strategies discussed in the former chapter:
keywords, synonyms, Boolean operators, quotation marks, and parentheses.
You can always alter your search strategy to fit the different search engines if necessary.
Here is a review of the main search engines:

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 PubMed
The search engine for MEDLINE, a bibliographic database compiled by the United States
National Library of Medicine.
This is the primary database for searching the medical literature.
The tool itself is free, although individual articles in it may not be.

Cochrane
Cochrane is a British institution with the mission of conducting and organizing scientific
research in health fields, especially in systematic reviews and meta-analyses.
We will typically include Cochrane as one of the search engines for our systematic
reviews and meta-analyses.
Cochrane is also the main authority on how to conduct systematic reviews and meta-
analyses. We will use their references anytime a question comes up on how to do a given
step in the process.
Cochrane Handbook for Systematic Reviews of Interventions:
https://training.cochrane.org/handbook/current
Cochrane Handbook for Systematic Reviews of Diagnostic Test Accuracy:
https://training.cochrane.org/handbook-diagnostic-test-accuracy

Scopus and Embase

Two medical databases developed by Elsevier, a Dutch editor focused on scientific
content in Medicine and other health-related sciences.
Both engines require a subscription for access. Check if you have access to either
Scopus or Embase through your institution.
These engines are very important for searching conference abstracts, which usually are
not indexed in PubMed, but are indexed in Scopus and Embase.
Although there are a few differences between Scopus and Embase, there is substantial
overlap between both tools, and it is not necessary to run the search on both platforms.
Searching for only one of them is enough. Embase is broader, so it is typically preferred.
Just like PubMed, Embase also has a controlled vocabulary.
PubMed: MeSH
Embase: Emtree
The use of controlled vocabulary is not essential in your search. Just like PubMed,
Embase includes the controlled vocabulary automatically.

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 LILACS
The largest search engine for Latin-American studies.
This database is free to access.
This is a much smaller database than PubMed or Scopus/Embase.
It would only be a relevant database for you if you are searching for topics that are
particular to Latin America, like Chagas disease or leishmaniasis.

Web of Science
This database is developed by Clarivate, an analytics company with multiple products in
science and business.
Clarivate is also responsible for calculating the famous “impact factor” of journals.
It is a collection of several international databases, for example:
Chinese Science Citation Database;
SciELO, Latin America, Caribbean, and Iberian countries’ database;
Arabic Regional Citation Index.
Web of Science requires a subscription for access. Again, if you want to use Web of
Science in your search (you don’t have to), check whether you have institutional access.

ClinicalTrials.gov
This is a registry of clinical trials, with the goal of improving access of the public to
clinical trials.
In the USA, it is mandatory to register clinical trials prospectively in this database. The
registry will include important protocol information, such as the target population,
study arms, planned interventions, etc.
This registration is mainly used to inform the study design and stage of development,
which is typically updated throughout the conduction of the study.
When the study is finalized, institutions and authors responsible for the conduction of
the study usually publish the results in a journal (indexed in PubMed and other
databases) before the results are updated on ClinicalTrials.gov.
Therefore, it is rare that we need to get the results of studies from ClinicalTrials.gov
since most of the results of clinical trials will be published in the literature, far before
they are updated in ClinicalTrials.gov.
However, theoretically, it’s possible that authors or sponsoring companies in charge of a
given clinical trial decide not to publish the results or delay the publication of results.
This may happen, for example, if the company has no intention of continuing the
development of a drug.
In these cases, there may still be a regulatory need to publish the results on
ClinicalTrials.gov, so you may only find some results there.

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 Therefore, although it is not strictly necessary, it is a good measure to check ClinicalTrials.gov
when you are conducting systematic reviews and meta-analyses. It may be uncommon, but
there is always a chance that you would find results there that have not been published in
indexed journals yet.

Gray literature
Asides from the previously mentioned databases, for some specific topics, it’s important
to search the gray literature.
Gray literature includes everything that is produced by government agencies, academic
fields, businesses, or industries that are not controlled by publishing companies.
For instance, if you are writing a systematic review of public policies on the
management of dengue fever in Latin America, there will probably be little information
about it on PubMed. So, it is important to search the websites of public health agencies,
send them emails, etc. All of this is considered gray literature.
Attention: for most systematic reviews and meta-analyses, there is no need to search
the gray literature. It is only if you search for some specific topic that may not be
available in indexed journals that you should look in the gray literature.
Importantly, there is no specific protocol on how the gray literature search must be
conducted. Each topic will have a different protocol of how to search for this data.

Putting it all together

After learning about all these databases, let’s put all of this together.
You will pick 3 databases for your search. I recommend PubMed, Cochrane, and Embase.
It is always good to check ClinicalTrials.gov as well, for the reasons mentioned
previously.
If you are searching for a topic particular for Latin America, add Lilacs also.
You can consider Web of Science as a substitute for Cochrane or Embase, or even as an
add-on (4th database), but it is not necessary.
If you are searching for anything that is outside of mainstream indexed publications, like
health politics or policies, you should search the gray literature.

Searching the other databases

Keep it simple. As discussed in class, I recommend that you simply remove anything that
is specific to PubMed, and then copy and paste it into the other databases.

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 This will save you so much time and it is highly effective.
Example: (“atrial fibrillation” OR atrial fibrillation [mh]) AND (“first-line” OR initial OR
naïve) AND (ablation OR radiofrequency OR cryoballoon OR cryoablation) AND
(antiarrhythmic OR “anti-arrhythmic” OR AAD OR amiodarone OR sotalol OR
flecainide OR propafenone)
In this case, you should remove atrial fibrillation [mh] from your search because it is
looking for MeSH terms, something that is specific to PubMed. Remember, you didn’t
even need this in PubMed to begin with, as we discussed in the last class. But, if you
decide to use it, remove the field tag [mh] before searching other databases.
Revised version: (“atrial fibrillation”) AND (“first-line” OR initial OR naïve) AND
(ablation OR radiofrequency OR cryoballoon OR cryoablation) AND (antiarrhythmic
OR “anti-arrhythmic” OR AAD OR amiodarone OR sotalol OR flecainide OR
propafenone)

Protocol registration

As you know, systematic reviews and meta-analyses follow a pre-established protocol.

This protocol includes a search strategy, medical databases to search, how to do study
triage, etc. In other words, all the different steps that we learn in the Meta-Analysis
Academy.
Therefore, it is important for the transparency of the whole process that this pre-
established protocol is documented somewhere. The idea and methods should be
registered prospectively, avoiding that results might influence the methods, which could
introduce bias.
When this registration is done, the idea of the systematic review/ meta-analysis
becomes public.
Registration of your protocol is not mandatory for publication, but some specific
journals may request it. It is becoming increasingly common to need this for publication.
There are specific platforms for registration. The most common one is PROSPERO, the
International Prospective Register of Systematic Reviews. Other platforms for this
include Research Registry, INPLASE, and protocols.io, among others.

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 PROSPERO is an open-access platform for registering systematic reviews and meta-analyses.
It is maintained by the University of York, in England.
To register your systematic review and meta-analysis in PROSPERO, just follow the
instructions on the website. This will include specific questions about how your meta-analysis
will be conducted, including some that we will still discuss later in the course, like statistics.
The Meta-Analysis Academy Publication Drive has a template for filling out your PROSPERO
registry. Feel free to use it and adapt it to your own idea.
Food for thought: what if your viable idea has already been registered on PROSPERO, what can
you do about it?
Think about this one. We will discuss more about it in CPT #5.

QUESTIONS

1. Among the following search engines, which ones must be included when the research question
involves topics that are particular to Latin America?
a) LILACS
b) Embase
c) Web of Science
d) ClinicalTrials.gov

2. The advantage of including Scopus or Embase as one of the medical databases in your search is:
a) Scopus and Embase are the only databases with controlled vocabulary.
b) Scopus and Embase include only high-impact journals.
c) Scopus and Embase include conference abstracts.
d) Scopus and Embase are the only public-access platforms.

3. Choose the correct alternative for the registration of a meta-analysis protocol:

a) Prospective registration in PROSPERO is mandatory for publishing a meta-analysis.
b) Prospective registration of a prespecified protocol is becoming increasingly common and many
journals require this to publish a meta-analysis.
c) Prospective registration should only be done when the writing of the manuscript is complete.
d) Prospective registration of a meta-analysis protocol can only be done in PROSPERO.

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 4. Regarding the gray literature, which alternative is correct?
a) The gray literature should always be searched in any meta-analysis.
b) The gray literature can be found on PubMed.
c) The gray literature searches for high-impact publications.
d) There is no universal protocol for how to systematically search the gray literature.

5. Which alternative is correct about search engines for different medical databases?
a) The search strategy may be modified to fit different search engines, but this may not be needed in
most cases.
b) The search strategy must be the exact same in all search engines.
c) The search strategy must be specific for each medical database, with the use of field tags that are
appropriate for each database.
d) Controlled vocabulary must be used for search strategies in PubMed (MeSH) and Embase (Emtree).

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 Answers

Exercise 1.
A. LILACS is the largest search engine for Latin-American studies. Consider including LILACS as a
search tool in studies with diseases of higher prevalence in Latin America.

Exercise 2.
C. Scopus and Embase are Elsevier platforms. They are not open access, but they have a major
advantage – they include conference abstracts. If an abstract has the data you need, it may be
included in your systematic review and meta-analysis. If you have many studies that are published
already, you may set conference abstracts as an exclusion criterion in your meta-analysis. It is up to
you.

Exercise 3.
B. The protocol registration has been increasingly requested by journals before publishing a meta-
analysis. The registration must be done before conducting the search and analyzing the results. This is
the reason why we put it at this stage in the Meta-Analysis Academy training program.

Exercise 4.
D. The gray literature must be searched for specific topics that are not typically found in indexed
databases. It is a generic term to represent everything that is produced by government agencies,
academic fields, businesses, or industries, but is not controlled by commercial publishing companies.
Consider using it in projects that include public health policies, for example. There is no universal
protocol on how the gray literature must be searched. It will depend entirely on the topic of the
search.

Exercise 5.
A. The search strategy may be modified for different search engines, but it does not have to. If you
build a simple, effective search strategy with synonyms, Boolean operators, parentheses, and
quotation marks, without anything specific to a given database, you may copy and paste it into
different search engines for many databases.

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