Transcript of video: Advanced PubMed: Literature searches for complex questions. While a simple search in PubMed will often find relevant articles,
you may find that sometimes you either need to be more thorough or that
the simple search did not retrieve what you hoped to find. When this is
the case, you may want to approach your PubMed search differently. This
video will walk you through the steps of conducting an advanced search
in PubMed. To do an advanced search, it is helpful to understand what is in
PubMed. Advanced searches also require that you learn to identify the
key concepts in your topic, identify subject headings relevant to your
topic, and use some PubMed search tools, including Search Details, the
MeSH database, and Advanced Search. First, what is in PubMed? We know that it is a database of citations
to journal articles in medicine and the related sciences. But is the
full text of the article also available within PubMed itself?
Unfortunately not. PubMed contains only the citations to articles, and
LINKS to the full text options. This means that you are only searching the citation information. This
includes the article title, journal title, authors, page number, volume
and issue, and the abstract if it’s available. You are also searching
something called the Medical Subject Headings, or MeSH terms assigned to
the article by indexers at the National Library of Medicine. These MeSH
terms are chosen from a list to describe what the article is about. So to get articles on your topic, it is important to choose search
terms that will best match the MeSH terms or medical subject headings. In PubMed, your search terms are automatically mapped to MeSH terms,
so many times this is done completely behind the scenes for you.
However, it is a good idea to check the Search Details to check to make
sure that the mapping has found a good MeSH term for your concept. If it
hasn’t, then you can look for a better subject heading in the MeSH
database. Before starting your search, it is important to think carefully about
your topic and what information you would like to find. So as you think
about your topic, take a moment to identify the key concepts in your
search. In our example of attitudes toward the HPV vaccine in developing
countries, our main concepts are likely the HPV vaccine, attitudes and
behaviors, and developing countries. To be facilitate better mapping, it is a good idea to search one
concept at a time. Let’s start with our first concept, HPV vaccine. After logging into HINARI and clicking on the PubMed link, we are at
the PubMed home page. We can type our first concept into the search box.
[type HPV vaccine] Note that as you type, suggestions may appear. These are not MeSH
terms, but are rather terms that other people have used. Generally, it
is safe to simply ignore these terms. After clicking search, the results appear. In order to determine
whether we were mapped to a relevant MeSH term, scroll down on the
results page to view the Search Details box. To make this area larger,
you can click on See more. On this page, note that our term hpv vaccine was mapped to the term
papillomavirus vaccine, which is relevant to our topic. Note that the
system also looked for the terms papillomavirus vaccine and hpv vaccine
in other fields of the citations to be sure to pick up newer citations. Since our terms were hpv and vaccine, it also looked for those in all
fields. So, we have been mapped to a MeSH term that is relevant to our
topic. We can now search for our second term, attitudes. Directly from this
search details page, we can type our term into the search box at the
top. [type in attitudes, and click search] Note that we are not searching within our set of citations about the
HPV vaccine, but are rather creating a second set of articles on our
second concept. We will combine these at the end. As we did with our first concept, we will now check the Search
Details box to see what kind of MeSH term we were mapped to for
attitudes [scroll down to search details]. In this case, we were mapped to a MeSH term for attitudes. This might
be a good term, or it might be too broad. If we want to determine
whether there could be a better MeSH term for our topic, we can scroll
back to the top of the page and change the search option to MeSH. This
will let us look directly in a database of MeSH terms for one that is
the best for our concept. [change search dropdown to MeSH, click
Search]. Our results are now MeSH terms that have something to do with
attitudes. Note that these are not citations, as we are now in the MeSH
database NoT the PubMed database. From this list of terms, it appears that there might be more relevant
subject headings for our topic. To see the definition of a term, click
on it. [click on attitude to health] This term is specifically about
attitudes to health, disease and the medical care system, and is more
specific to our topic than simply the term attitudes. Scrolling down on a MeSH term page will tell us more about the term.
From the outline structure on the page, we see how it fits in with other
MeSH subject headings. This is a broader term than health knowledge,
attitudes, and practice, and includes such other terms as patient
acceptance of health care and treatment refusal. These would be good
terms to include in our search. In PubMed, when you search with a MeSH term, the system will
automatically include citations that are indexed to terms that are
narrower than your term, unless you tell it not to. So if we search
using this term, we will automatically also find citations that are
about these narrower topics. Once you have identified a MeSH term you would like to include in
your search, you can send it directly from the MeSH database. [scroll
back up] Simply click on the Add to Search builder button, then click on
Search PubMed. This takes you back to the results page in PubMed for
your selected term. We are now ready to search for our last term, developing countries. [type in developing countries, click search]. Again, it’s important to check the Search Details box to determine if
this was mapped to a relevant MeSH term, and we see that it was. If it
had not been, we could return to the MeSH database and find the
appropriate term. In this case, we can now move on to combine our sets
together. To combine sets, click on the Advanced search link [click Advanced].
This page is where you can come to find your search history for the
session. To combine sets from the search history, simply click ADD next
to the best set from your searches. We will choose the sets associated
with hpv vaccine, attitude to health, and developing countries. This
will place the sets into the search builder. Remember that AND is used to find a set of articles that has all of
your terms, and OR is used for finding a set of articles that has any of
your terms. In this case, we will use the defaule AND, because we want our set of
citations to include all of our concepts. We will now click Search
[click Search]. As this is a fairly narrow topic, there are only a few results. In
Video 3, we used the Limits page. Here, using Limits is probably not
necessary as there are not many results to look through. Instead, we may
want to look at the filters for Free Full Text and HINARI to see what
can be accessed in full text. In summary, to conduct an advanced search, you should first identify
your main concepts. Search one at a time. Check Details to see if you
were automatically mapped to a good MeSH term, or medical subject
heading. If you weren’t, go to the MeSH database to find a better term and send it to the search box. Combine your best sets in Advanced search using ANDs and Ors. Apply limits if necessary. And look for HINARI and free full text buttons to connect to the
full text of articles.
Transcript of video: Using PubMed through HINARI can help you find articles on a topic and
connect to HINARI or other free full text versions of them quickly. PubMed is the US National Library of Medicine’s search engine for the
MEDLINE database. It searches over 20 million citations to journal
articles in medicine, basic sciences, nursing, dentistry, and related
biomedical fields. HINARI links to a special version of PubMed that makes it easier to
find full text articles in HINARI and articles that are available for
free on the Internet. Let’s click on this link to open PubMed. The example topic is malaria. Type a term into the search box. As you type, terms other people have
searched for appear below. These are not recommended or preferred
terms, so it is best to ignore these. Click search. This search was very broad and retrieved many results. PubMed has
many citations, so it helps to be specific. For example, if I am
treating pregnant patients with malaria, then I could improve my search
by adding AND pregnancy after the initial search term. This refines our
search toward our topic. Note that using AND between search terms narrows your search to only
those citations that have both concepts. Using OR between search terms
broadens your search to retrieve citations with either concept. Once you have a set of articles on your topic, use filters to refine your results more. Filters appear to the left of results. I can narrow my search by date (such as the last 5 years),
publication type (such as clinical trials), and even patient
characteristics. More filters are available by clicking show additional
filters, for example age. If we were interested in articles on effects
of maternal malaria on infants, we would choose the infant filter. If we
want articles on malaria in either mothers or infants, we could check
limits for adults and infants. Be careful not to choose full text or free full text yet. Choosing
these may remove some of the articles that you could get through HINARI.
I now have results that are clinical trials from the last ten years about malaria and pregnancy in adults and newborns. The default view for results is called the Summary view, and lists
only the basic information about the article. If you would like to read
more, click on the article title. This will take you to the abstract, if
it is available.
This view also shows you access options. The first button is the
publisher button. The second is the HINARI button. To get to full text,
click on the HINARI button. Look for the PDF option for the easiest saving and printing. The PDF
looks like the paper version, has full-sized graphics, and page numbers.
Other journals will look different, as they may be published by
different companies or societies. To get back to the results, close this journal window. Then click back on the browser. Some articles will be available for free – see the Free in PMC note
below the citation. This article is available for free from the journal,
through HINARI, and for free in PubMed Central, the open access
repository tied to PubMed. Click on any of these buttons to get to the
full text. Other articles may not be available through HINARI or for free. If you see NO buttons on an abstract, then it is not available. If you see only a publisher button (NOT HINARI and NOT free full
text), then you will likely be confronted with the option to buy the
article, rather than the full text itself. If you want to browse only those citations that you know are
available via HINARI or for free, try the filters to the right of the
results.
• The HINARI filter limits you to citations available in HINARI journals
• The Free full text filter limits you to citations available for free.
Browse both lists, as there may be overlap and unique citations between the lists. This concludes the video on How to Search PubMed in HINARI. For more
advanced searching techniques, see the video on Advanced PubMed
Searching.
Transcript of video: HINARI provides access to the full text of many journals. This video
will demonstrate how to find the full text of a specific article. Go to HINARI at who.int/hinari and click to log in. If you do not know your institution’s user name and password, contact the librarian at your institution. Be sure to citation information for the article. This includes the
article title, authors, journal name, publication date, volume, issue,
and page number. This information will help you drill down to the
article. As an example, we will look for this article on stillbirths
from the Lancet. Start with the journal title, Lancet, then browse to the volume and
issue. Scroll down to find the correct page number and the article of
interest. Not all journals look alike. If you do not easily see the option to
browse by year or volume, look for language like Browse Archive, or Past
Issues. Here is the article we are looking for. Click on PDF if you would
like to print or save your article to your computer or flash drive.
Click on the Print icon to print the document, and the save icon to save
the document to your USB flash drive or computer. If you do not find the journal or the article that you are looking
for, it may not be available. Since some journals offer articles for
free, the PubMed Single Citation Matcher is a good second place to check
for full text. Return to the HINARI content homepage. then Click on the “Search inside HINARI full-text using PubMed” link.
This will open a new window for PubMed. In this example, we will look for this article from the Ghana Medical Journal on congenital malaria in newborn twins. Now click on Single Citation Matcher under PubMed tools.
Enter at least two pieces of information from your citation and click Go. This is the reference in PubMed. To connect to the full text, look
for the HINARI button, or a link to Free Full Text. This article is
available for free through PubMed Central. If you do not see a HINARI or free full text button, then the article
may not be available through HINARI or for free. If this is the case,
talk to your librarian about access options, including whether the
article might be available in print or from another institution.
At times, you may encounter trouble accessing the full text of an article or resource that you think should be available.
When trying to access a journal, you may be prompted to sign in or
purchase an article that should be available. Your HINARI institutional
username and password will not work.
These access problems can be caused by:
1) failure to LOGIN with the institution's User Name/Password
2) technical problems at the Publisher's website
3) problems with local systems (such as the configuration of the institution’s firewall or browser)
OR
4) The publisher has not authorized access – which is more likely to be a problem for Group B countries
To confirm that you have used the institutional User Name and Password
correctly, check that you have the ‘You are logged in’ message on the
HINARI homepage.
This is also confirmed in the address or URL search box of the web
browser. If properly ‘authenticated’, you will see a URL that begins
with: hinari-gw.who.int/whalecom...
Double check the access to a journal by going to the title in the
‘Journals by title A-Z’ list and verify the years of volumes available.
When viewing any page of the Journals by title A-Z list, the green box
notes if your institution has access to the contents of the journal. The
! notes that your institution is denied access (predominantly Group B
although some Group A).
The ‘years of volumes’ available are listed after the journal title.
If you are denied access to a full-text article despite the green box, please follow these instructions.
1. First Double check your login
2. Contact HINARI at hinari@who.int
Please let HINARI staff know of problems by emailing hinari@who.int. so
that they can communicate with the Publisher and resolve the problem.
In your email…
• include your institutional User Name,
• include the name of the journal(s) and other details.
• include a screen capture that contains the URL (Internet address) of the journal
Here is an example of a screen capture sent to hinari@who.int It
includes that This item requires a subscription and the publisher
requested that the user Sign in or Purchase Short-Term Access.
• It also includes the URL of the journal. This information is valuable to HINARI staff
• You can create a screen capture by clicking on the Print Screen key
while viewing the webpage of the journal. Then paste (edit/paste or
control/v) the material into a word processing document and send as an
attachment.
This additional screen capture notes that Journals by Title A-Z list shows this article should be available.
Sometimes the access issue may be related to institutional firewall problems.
• Please check with your computer department to make sure the institution’s firewall does not block proxy servers.
• The computer system must be able to access HINARI’s proxy server.
• Insure that you are permitted access to the HINARI IP address through
your institution’s firewall. Otherwise, you will not be able to login
properly and access HINARI’s full-text articles.
In summary, access problems can be frustrating, and could have multiple causes. To determine what the problem might be…
• First confirm that you are signed into HINARI
• Look for the icons that indicate that you should have access to the resource.
o In HINARI, this is a green box.
o In PubMed, this is either the HINARI icon or the free full text icon
• Email HINARI with details of the problem.
• Some users may have to work with their computer departments to ensure
that the institution firewall is permitting HINARI access.
HINARI is a free or low-cost digital library of scholarly journals and
books in biomedical and related social sciences. Through HINARI,
eligible users can get to thousands of electronic journals and numerous
online indexes, databases and books to help make clinical decisions,
further education, and conduct research.
The HINARI Access to Research in Health Programme was set up by the World Health Organization together with major publishers.
Through the program, not-for-profit institutions in developing countries
can have free or low-cost access to peer reviewed content online. As of
2012, more than 150 publisher partners are offering more than 15,000
information resources in HINARI and many others are joining the
programme.
Country eligibility is based on three international measures of gross
national income and development, and eligible countries either fit under
Group A –free access, or Group B – low-cost access. The HINARI
website - who.int/hinari contains detailed information about eligibility and registration.
Institutions, not individuals, can register with HINARI.
Once the institution is registered, all permanent and visiting faculty,
staff and students can access HINARI through their institution’s
username and password.
If you do not know your institutional username and password or if your institution is registered, please contact your librarian.
All resources within HINARI are accessible from one gateway. Start at who.int/hinari and click to log in. Once you type in the institutional username and password, you will come to the starting page.
On the center of the screen, you can browse available journals and books by title.
You can also browse the content by subject, language or publisher.
Subject browsing may be very useful for seeing what is available in your
area. Click on the content tab to go back.
On the starting page, you can also choose to search for articles in the
PubMed database. This is a special version of PubMed that connects to
the full text of articles through the HINARI collections or that are
available for free.
On the right, you can access additional HINARI content. You can search
other article databases, including some that offer full text, such as
African Journals Online, or coverage in different subject areas, such as
CINAHL (the cumulative index to nursing and allied health literature)
and Scopus.
Under Reference Sources, numerous online reference sources, encyclopedias, manuals and textbooks are available.
And under Other Free Collections, you can easily connect to other free collections of biomedical and scientific content online.
This is the first in the video series will take you through the steps of
some common tasks, such as finding the full text of an article,
searching PubMed, and dealing with access problems and solutions.