Transcript HINARI Short Course Table of Contents • • • • • Background and Do’s and Don’ts Searching Strategies & Boolean Operators Sign In Procedures HINARI Website Features PubMed Searching from.

HINARI Short Course
Table of Contents
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Background and Do’s and Don’ts
Searching Strategies & Boolean Operators
Sign In Procedures
HINARI Website Features
PubMed Searching from HINARI
– Overview of PubMed Website
– Filters and Advanced Search
– My NCBI
• Training Materials Overview
HINARI
• The HINARI Access to Research Programme is
coordinated by the World Health Organization
(WHO)
• HINARI is a public-private partnership between
the WHO, publishers and other health care
content owners
• To provide biomedical and health care research
and guideline information to non-profit academic
and research institutions, governmental and
policy making departments in low income
countries.
• AGORA (agricultural research) and OARE
(environmental research) are similar programs
http://www.research4life.org/
• More than 100 countries, territories and areas
• HINARI: health research (12700 journals, 24900
books and 70 information resources, 5400 registered
institutions) www.who.int/hinari/en/
• AGORA: agriculture research (3500 journals, 3400
books, 20 information resources, 2300 registered
institutions) www.aginternetwork.org/en/
• OARE: environment research (5300 journals, 11100
books, 40 other information resources, 2500
registered institutions) www.unep.org/oare/en/
• ARDI: development and innovation research (2000
journals, 500 books, 80 registered institutions)
www.wipo.int/ardi/en/
updated 2013 08
Eligibility (01 2014)
1. Countries, areas, or territories with a total GNI above
US$ 1 trillion are not eligible for HINARI regardless
of other factors
2. Core Offer Group A - Free Access
All countries, areas, or territories fulfilling any of the
below criteria:
a. UN Least Developed Country List and/or
b. Human Development Index (HDI) is at or less than
0.50 and/or
c. Total Gross National Income (GNI) is at or less
than US$ 150 billion where:
HDI is at or less than 0.63 and/or
Gross National Income per capita (GNIpc) is at or
less than US$ 1600
3. Core Offer Group B - Fee access with $1000
annual fee per institution:
a. Total GNI is at or less than US$ 1 billion
and/or
b. Total GNI is at or less than US$ 20 billion
where GNIpc is at or less than US$10,000
and/or
c. Total GNI is at or less than US$ 180 billion
where:
HDI is at or less than 0.67 and/or
GNIpc is at or less than US$ 5000
Who is Eligible for R4L Programmes?
Primary Target Audiences
Eligible categories of institutions are:
• national universities
• research institutes
• professional schools (medicine, nursing, pharmacy, public
health, dentistry)
• teaching hospitals
• government: ministries and agencies
• national medical libraries
• locally based non-governmental agencies
All permanent and visiting faculty, staff members and students
are entitled to access and can obtain the institutional User
Name and Password.
Partners
 Principal Publishers
 Program Partners
 Elsevier Science
 Springer
 Wiley-Blackwell
 Sage
 Taylor & Francis
 Lippincott/Williams & Wilkins
 BioOne
 Oxford University Press
 Nature Publishing
 Other science/technical/
medical publishers
 World Health Organization - WHO
 Food and Agriculture Org. – FAO
 United Nations Environment
Programme – UNEP
 World Intellectual Property
Organization - WIPO
 Yale University Library
 Mann Library/Cornell University
 International Association of
Scientific, Technical and Medical
Publishers – STM
 Information Training and Outreach
Centre for Africa
 National Library of Medicine
 Microsoft
 Librarians Without Borders®/MLA
http://extranet.who.int/hinari/en/partners.php
HINARI Do’s/Users
• Material owned by the Publishers made
available through HINARI can be used by
Authorized Users or Walk-in Users
– An Authorized User: an institution’s or
government department’s employee,
permanent or visiting faculty, or student
– Walk-in User: anyone who comes to the
Institution’s premises and is permitted by the
Institution to access services there
HINARI Do’s/Articles
For participants:
• institution may supply printed or digital
materials (documents) to the institution’s
employees, faculty members, students or
another Authorized User
• remote access is permissible but limited to
computers owned personally by employees
or by institution
• Professors/lecturers can place publisher’s
material in print Course Packs or placed in
Electronic Reserves for students (delete after
the end of the course)
HINARI Don’ts/Articles
• Downloading/Printing: users cannot
download complete journal issues or books
(per journal issue or book, 15% limit)
• Course Packs: professors/lecturers
– cannot make a profit from the publisher’s
material
– can charge for cost of printing only
HINARI Don’ts/Articles
• Document supply: Cannot distribute
documents obtained through HINARI to any
other individuals or organizations outside the
registered institution
• Document fees: The institution may not
supply the document for a fee except to
recover cost of printing
• Uploading: Cannot upload the material to or
post to a publicly available website or
elsewhere
HINARI Don’ts/Content & Software
• Cannot modify, adapt, transform or create
any derivative work from the publisher’s
material, software or hosting agent or
tamper with the access software
HINARI Don’ts/Access
• Do not give the Publisher’s Material or User
Name/Password to other individuals or
institutions
• if others are interested in HINARI, send them
to their institutions’ libraries
• Do not access HINARI while traveling outside
the country
• Do not put the User Name/ Password on the
Institution’s website or any other Internet page
• Do not share or publish the ID and password
through public sites on the Internet: Groups,
Wikis or Blogs
• can put a link to initial page of HINARI or have
information about HINARI
Suggestion
• Modify the ‘Do’s and Don’ts Template’ (Word
document) for your institution
• Print copies and distribute to HINARI users when you supply the IDs and Passwords
• Have each new users read the ‘Do’s and Don’ts’
and sign that they understand and accept the
limits
• You will have fulfilled your responsibilities as a
provider of the Institutional IDs and Passwords
Write the NameHINARI USAGE POLICY
Institution: _______________
Institutional ID: ___________
Password: ______________
HINARI DO’s
•Material owned by the Publishers made available through HINARI can be used by Authorized Users or Walk-in Users
•An Authorized User is an institution’s or government department’s employee, permanent or visiting faculty, or student
•Walk-in User are anyone who comes to the Institution’s premises and is permitted by the Institution to access services there
•Institution may supply printed or digital materials (documents) only to the institution’s employees, faculty members, students or
another Authorized User
•Remote access is permissible but limited to computers owned personally by employees or by institution
•Publisher’s material may be placed in electronic reserves for students to access in specified education courses (delete after the
end of the course)
•Course Packs: professors/lecturers may make copies in print or digital form of the Publisher’s Material for use by students
HINARI DON’Ts
•Do not put the ID and password on the Institution’s website; a link to the initial page of HINARI or information about the program
is acceptable.
•Do not share or publish the ID and password through public sites on the Internet: Groups, Wikis or Blogs.
•Do not give the Publisher’s Material or ID/password to other individuals or institutions (if others at your institution are interested,
send them to the Library or Director)
•Do not access HINARI while traveling outside the country
•Downloading or printing: users cannot download or print complete journal issues or books (per journal issue or book, 15% limit)
•Course Packs: professors/lecturers only can recover the cost of producing such course packs from the students; cannot make a
profit from the Publisher’s Material
•Document supply: cannot distribute documents obtained through HINARI to any other individuals /organizations outside the
Institution
• Uploading: cannot upload/post the material to a publicly available website or elsewhere
•Content and Software: cannot modify, adapt, transform or create any derivative work from the publisher’s material, software or
•hosting agent or tamper with the access software
SIGNATURE:___________________________________
DATE:_____________PRINT NAME:___________________________________
For copy of this document, see HINARI_Usage_Policy_Template...doc
Last updated: 2010 12
Exercise 1
Complete exercise 1 in the workbook.
Example (Steps 1-4)
1.
2.
3.
4.
Ask: What health problems are associated with water pollution?
Need: scholarly primary research
Main Concepts: health, water, pollution
Select terms:
– Broader terms: ‘health’, environmental degradation’,
‘agricultural management’,
– Synonyms:
health, illness, disease, etc.
water, rivers, lakes, sea, domestic water, etc.
pollution, ‘oil spills’, chemical, biological, toxicity, etc
– Alternative spellings: none
– Plurals: river(s), lake(s), disease(s)
– Capitals: e.g. name of a specific lake, disease, region
Types of Sources
Select a Source (Step 5)
Tertiary Sources
ADVANTAGES
DISADVANTAGES
Easy access
Lag Time
Ease of use
Outdated
Concise
Incomplete information
Relatively inexpensive
Incorrect interpretation
Secondary Sources
ADVANTAGES
DISADVANTAGES
Rapid access to the primary literature
Lag time
Generally high standard journals
Command language varies
Ability to perform complex searches
Proficient search skills are needed
Routine updates on selected topics
(alerts)
Can be expensive
Primary Sources
ADVANTAGES
DISADVANTAGES
Original data
Large volume data
Unbiased information
Time consuming
Search Construction
Boolean (Search) Operators
• Connect terms and locate records
containing matching terms
• Inserted in a search box – AND, OR, NOT
• Must be in UPPERCASE when used
• AND, NOT operators are processed in a
left- to right sequence. These are
processed first before the OR operators
• OR operators are also processed from leftto-right
AND Operator
(to combine two concepts)
the AND operator is used to combine two
concepts e.g. hip AND fracture – in the
shaded area
AND Operator
(to combine three concepts)
the AND operator is used to combine three
concepts e.g. hip AND fracture AND elderly –
in the shaded area
OR Operator
(info containing one or other term)
renal OR kidney – in the shaded area with the
overlap in the middle having both search terms
NOT Operator
(in one term or the other)
pig NOT guinea – in the shaded
area; eliminates items in 2nd term
(guinea) or both terms
Other search engine functions
• Phrase or proximity searching: “…” or (…)
– allows you to search for an exact phrase
“information literacy”
prevention and (malaria parasite)
• Truncation/wildcards: * or $
– allow you to search alternative spellings
child* for child OR childs OR children
parasite* for parasite OR parasites
• Alternate spellings: ?
– can be used to substitute for characters anywhere
in a word
wom?n would search for “woman” and “women”
Africa AND (HIV OR tuberculosis)
HIV
tuberculosis
Africa
Africa AND (HIV or tuberculosis) – in the shaded area
The (OR) operator retains items in each term and the AND
operator is used to combine two concepts
More Search Techniques
• Field Specific Searching
– author, title, journal, date, url, etc.
• Language Restrictions, Humans or Animals, Gender and
other limits
(to be discussed in PubMed FILTERS)
• Relevancy Ranking
– a grading that gives extra weight to a document when
the search terms appear in the headline or are
capitalized
– every found document is calculated as 100% multiply
by the angle formed by weights vector for request and
weights vector for document found
Evaluating Web Information
•
Criteria for Evaluation
-
•
Accuracy
Authority
Currency
Coverage
Objectivity
Criteria for evaluating Health Information
http://www.nlm.nih.gov/medlineplus/evaluatinghealthinformation.
html
Additional Resources
• A User's Guide to Finding and Evaluating Health
Information on the Web Medical Library Association, USA
http://www.mlanet.org/resources/userguide.html
• Evaluating Internet Health Information: a Tutorial National
Library of Medicine, USA
http://www.nlm.nih.gov/medlineplus/webeval/webeval.html
• How to evaluate Health Information on the Internet
National Institutes of Health, Office of Dietary Supplements
http://ods.od.nih.gov/Health_Information/How_To_Evalu
ate_Health_Information_on_the_Internet_Questions_an
d_Answers.aspx
Google Search: Dengue Fever
The Google search engine
This is the Google search engine. Type
your query into the Google Search box
and click on the search button. We
have typed HINARI into the search
box. Google’s URL is www.google.com
Google Scholar provides a simple way to broadly
search for scholarly literature. You can search across
many disciplines and sources: peer-reviewed papers,
theses, books, abstracts and articles, from academic
publishers, professional societies, preprint repositories,
universities and other scholarly organizations. Note the
Advanced Scholar Search option.
HINARI INARI HINARI1`
In Google Scholar, the HINARI results are
either an article about the program or one
with HINARI being the author’s name.
Exercise 2-3
Complete exercise 2-3 in the workbook.
HINARI Website
This is the initial page of the HINARI website.
Note in the left-hand column, that there are links
to the Access to Content, Register, FAQs and
Training Materials pages. To access the HINARI
website, enter the URL http://www.who.int/hinari/
Initially, we will look at the Eligibility page.
Your institution must be registered for you to gain
access to the full-text electronic resources.
Click on the Register for HINARI link to access
the step-by-step guide – to see if your institution
is registered or must complete this process.
Note: for detailed information on eligibility and
registration, go to Module 3 – HINARI
(Research4Life) Eligibility and Registration:
http://www.who.int/hinari/training/en/
This is the step-by-step guide to completing the
Research4Life online registration process. First,
you need to make sure your institution is not
already registered. There is a link to check the
Registered Universities and Professional
Schools:
www.who.int/hinari/faq/registration_and_eligibility
_registered_universities/en/index.html
http://registration.research4life.org/register/default.aspx
From this page, institutions can register for 3
different Research4Life programmes*. Check
eligibility of your institution.
*ARDI currently has a separate registration
page: www.wipo.int/ardi/en/register_form.jsp
Note the detailed contact information that is
required (Registrant, Librarian/Information
Liaison, Director and Computer Support
Officer). Please make sure you completely fill
out the REQUIRED information or the
registration cannot be properly processed.
Remember only one registration per
institution is required. If not registered,
complete form and click on Send
Registration. Once the application is
approved and processed, the library
and director contacts will receive the
HINARI welcome message. All
members of the institution can use the
institution’s User Name and Password.
We have displayed the access page to the
Registered Universities and Professional Schools
by Countries, Areas and Territories PDF
documents for HINARI, AGORA and OARE.
To download the PDF file, click on the HINARI list.
This is one of the pages of the 'Institution profile' that you will
not be able to view.
For updating contacts, please provide the full names of your
country, institution, librarian and/or director, and his/her e-mail
address(es), to the trainers or to HINARI via [email protected] .
We now have opened the Eligibility page. Note the descriptions
of the Group A (free access) and Group B (low-cost access). The
countries, areas and territories in each group are listed at the
bottom of this page. Group B institutions that cannot or choose
not to pay the annual fee will have free access to some resources.
This page lists the publishers
who have made some resources
available to Group B institutions
that cannot or choose not to pay
the annual fee.
Login to the HINARI website by clicking on
LOGIN.
Note: If you do not login into HINARI, you
will not get access to the full text articles.
We will need to enter our HINARI User Name and Password in
the appropriate boxes, then click on the Login button. To have
access to the full text articles, you must properly sign in.
If you do not use the Internet Explorer Web browser, this slide
will not appear (as of 01 April 2014). If you use Internet
Explorer, you will continue to have a two-step login process.
Repeat the Login process on this
2nd page and you will be redirected
to the HINARI Contents page.
Once logged-in, you will be taken into the
Access the content sub-page of the website.
Note the ‘Logged in from: Test Account’
message. That line will list your country. This
proper login also can be confirmed by the
hinarilogin.research4life.org/... url
If you fail to use the Login page, you will have a
second option on the Content page.
Note the key access choices – Journals
collection, Books collection, and, on the
horizontal frame, Subjects, Languages,
Publishers and a link to the Training Materials.
Also note the Register for HINARI link to a stepby-step guide plus other information.
In this example, we opened the Browse
Subject ‘HIV/AIDS’ listing (without the proper
login) and clicked on the Accessible Content
option. Of the initial17 journals titles listed,
only 2 are Full access to this content for
everyone while there are 15 that are not
accessible You must log in to access HINARI
to have full access to this content.
Journals can be accessed by title from an
alphabetical list.
For this exercise, click on ‘L’ from the A-Z list.
Note: there also is a View complete list of
journals option although this drop down menu
does not have hypertext links to the journals.
We have displayed the ‘L’ journal list. Click on the title for The Lancet. The default is
the Accessible Content page. This and the All Items displays will be discussed in
subsequent slides.
The green box notes access to the contents of the journal for you while the ! Notes
specific journals that are titles not included in publishers’ offer to your institution. Note
that the ‘years of volumes’ available are listed after the journal title.
Accessing journals by title 4
Another window will open at the
journal publisher’s website usually
with access to the current issue.
For each article, there are three options:
[Abstract], [Full Text] or [PDF] formats.
You can get the article in Full Text or HTML
format that includes links to sections of the
article, bibliographic citations or related articles.
With the PDF or Portable Document Format, you
will receive a scanned image of the article. This
format is similar to the traditional print option .
To download a PDF document, you will need a
copy of the Adobe Acrobat program which can be
download freely from the Adobe website:
www.adobe.com
A helpful hint for searching within any letter of
the Journals content A-Z list is to click on Control
F. This opens a new search box. In the S
listing, we have put surgery into the box and
there are 19 titles with this word. To view other
titles, use the scroll up and down buttons.
Full-text Article Access Problems
Using the Journals collection A-Z list, we are
attempting to access a full-text article from
the Blood.
Although HINARI users should have access
to this journal, we will use this as an example
of ‘what could go wrong.’
Access problems can be caused by:
1) failure to properly LOGIN with the institution's User Name/Password
2) technical problems at the Publisher's website
3) or problems with local systems (configuration of user institution’s
firewall, configuration of browser)
4) Titles not included in publishers’ offer
Consequently, you may see a message on the Publisher‘ denying
access and requesting LOGIN or payment for the specific article.
Note: Your HINARI institutional ‘User Name/Password’ will NOT work.
To confirm that you have used the institutional User Name and
Password correctly, check that you have the ‘Logged in from’
message.
This also is confirmed in the address or URL search box of the
web browser. If properly ‘authenticated’, you will see a URL that
begins with: hinarilogin.research4life.org/... url
Institutional Firewall Problems
In this situation, a proxy server is blocked by the
institution’s firewall. 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 IP 158.232.242.4
through your institution’s firewall. Otherwise, you
will not be able to login properly and access
HINARI’s full-text articles.
NOTE: If you have problems when you are accessing a full-text
journal from HINARI/PubMed (not via the links from the principal
HINARI page), there is one other step to check.
If you are unable to access an article from a journal via the ‘Link
Out’ icons in HINARI/PubMed, double check this by going to the
title in the Journals collection A-Z list and also verify the years of
volumes available.
When viewing any page of the Journals collection A-Z list, the green box
notes if your institution has access to the contents of the journal. The ! notes
the titles not included in the publishers’ offer to your institution.
If you are denied access to a full-text article despite the green box, follow
the instructions in the next slide. Note that the ‘years of volumes’ available
are listed after the journal title.
This is the example of the screen capture that was
attached to the email message for [email protected]
For the JEM article, it noted that This item requires a
subscription. The publisher requested that the user
Sign in (User Name and Password for individual
subscription) or Purchase Short-Term Access.
Note: this screen capture includes the URL of the
journal. This information is invaluable to the HINARI
staff who will try to resolve the access problem.
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.
Double check that you have completed the HINARI
LOGIN. If this is not the problem, notify HINARI staff
([email protected]) so that they can communicate with the
Publisher and resolve the problem. This example is an
email received from a HINARI user in Uganda.
Note: make sure you include your institutional User Name,
the name of the journal(s), publisher(s) and other details.
Also include a screen capture that contains the URL
(Internet address) of the journal (seen next slide).
This additional screen capture notes that the
journal is listed on the J page of the Journals
collection A-Z list, that the requested journal issue
is available and that, by the green box, the
institution should have access to the journal.
If the HINARI authentication system had worked
properly, the user would have had access to the
journal article. Updated 2013 11
We now will discuss one other
potential access problem. This is in
HINARI/PubMed searches. If you
use the Abstract format from the
Display Setting, the links to full-text
articles will be displayed.
PubMed uses the ‘Link Out’ software to access
the full text articles. If this does not work
properly, you will not have access to the article
and be asked enter an individual user name and
password or pay a fee.
Follow the same procedures listed in the
previous slides. At times, an article will not be
accessible from HINARI/PubMed but is available
from the Journals collection A- Z list.
Updated 2013 11
Click on the link to find journals by
Subjects. From the drop down
menu, we will select Parasitology
and Parasitic Diseases.
An alphabetical list of Parasitology and
Parasitic Diseases journals is now
displayed with links to the journal
websites.
Click on the title Journal of Parasitology
After the title of the journal, the available
volumes/issues are listed.
By clicking on a journal title, you
will open the journal in a new
window: Journal of Parasitology.
For the Parasitology and Parasitic
Diseases journals, we have opened
the All Items list for an institution
where all the material is not included
in the publishers’ offer.. Note the white
box with the exclamation point – for
journals that cannot be accessed.
We have displayed the Browse
publisher drop down menu. This
You have full access to: list for an
institution where all the material is
included in the publishers’ offer.
We have displayed the Browse publisher
– Nature Publishing Group Accessible
Content list. It is an example from a
country with no exclusions - noted by the
green boxes.
We now will open the Publishers
list of journals as an institution that
does not have full access to the
publishers resources.
We now have opened the Browse publisher – Springer list as an institution where the titles are not included in the
publisher’s offer. The default is the Accessible Content page
and no journals are listed. If you click on the All Items
option, you can view the journal titles that your institution
does not have access to – for this publisher. Check other
publishers to see if the journals are accessible or not.
We now have opened the Browse
publisher – Springer All Items list.
For this institution where the titles
are not included in the publisher’s
offer, all the titles have the !.
To find books by title, click on the appropriate
Books collection alphabetical letter.
Note that there is a View complete list of
books option although this drop down menu
does not have hypertext links to the specific
titles. You will need to go back to the Books
collection A-Z list to open any e-books.
Now opened is the O list from the Books
collection A-Z list. This example is for an
institution where the titles are included
in the publishers’ offer.
We now have opened is the O list from the Books
collection A-Z list - for an institution where many
titles are not included in the publishers’ offer.
Note that there are only 2 items in the Accessible
Content list. In the All Items display option, most
of the titles will have the white box with the
exclamation point.
The Oxford Textbook of Medicine is one of the
foremost international textbooks of internal medicine.
It provides practical guidance on the clinical
management and prevention of disease, with indepth coverage of the traditional specialty areas.
Scroll down this page to the ‘expandable’ table of
contents that details the contents of each topic.
From the HINARI Content page, you
also can open the Search inside
HINARI full-text through database
and article searching, Reference
sources and Free collections lists.
Note: Many of these resources are
underutilized by HINARI users as
most individuals concentrate on
obtaining full-text journal articles.
Via clicking on the Database and article
searching link, we have opened the Browse
databases A-Z list.
Similar to other access points, there are the
Accessible Content and All Items listings
that depend on the Publishers’ exclusions.
Now we have clicked on the
Reference Sources link and opened
the Browse reference sources A-Z list.
Many of these resources contain fulltext information on a variety of topics.
Cochrane Library contains high quality , independent
evidence for health care decision making. It includes
numerous access options including via keyword, MeSH terms
and category listings. Cochrane Library is one of 3 sources of
information on evidence-based practice in HINARI.
From the Free Collections drop down
menu, you can access other free e-journal
gateways and be able to obtain full-text
articles. We will examine one of these –
Highwire Free to Developing Economies.
HighWire Press 3
This is the HighWire Press initial page. From this
site, we can locate articles or journal titles or
subjects and set up an email alert.
The Free Access to Developing Economies link is
located on the initial page. Also of interest is the
Free full-text content link.
There is a link to both pages in the Free
Collections drop down menu on HINARI’s
Contents page.
Note: You can access the HighWire Press
full text articles since this publisher
identifies computer (IP) addresses from
eligible countries. This is the ONLY
exception to not needing to use your
institution’s User Name and Password.
You now have entered the Free
Access to Developing Economies list
of HighWire Press.
As noted, the access is based on the
computer's IP Address and you can
go directly to the site using the url.
Within HighWire Press, we have
entered the Free Online Full-Text
Articles page.
HighWire Press 4
Note that some journals are a free
site and others have free articles after
a set period of time.
The HINARI eligible country access is
a different mix of titles.
We have accessed the Current Issue of
the American Journal of Epidemiology
with the Table of Contents and, for
articles, full Text (HTML) and PDF
options to specific articles plus an
internal keyword search engine.
We have opened the Directory of
Open Access Journals (DOAJ). In
the search box, enter hospital
infections and developing countries
and check the Articles box.
The results for this search
in DOAJ are 89 articles.
We have opened the Browse option
where, you can search for journals
by title, subject, country, license and
publication charges.
Exercises 4-7
Complete exercises 4-7 in the workbook.
PubMed Overview
From the HINARI Content page, we can
access PubMed by clicking on Search
inside HINARI full-text using PubMed.
Note: If you do not properly sign on, you
will not have access to full text articles
from the HINARI/PubMed database.
In October 2009, the PubMed display was redesigned in a simpler and more intuitive fashion.
Remember to access PubMed through HINARI or
you will not have access to the full-text articles.
The bottom part of the initial PubMed page that is
displayed here contains hypertext links to numerous
databases and tools produced by the U.S. National
Center for Biotechnology Information (NCBI).
Note the Bookshelf option that gives you access to
numerous full text e-books.
The Search box on PubMed is active. Place your
search statement in the box.
In this example, we enter a search for malaria
infections AND Africa into the Search or query box.
To execute the query, click on the Search button.
Results of the search are displayed in the main body of the
page in Summary Format, 20 Items per Page and Recently
Added Sort by options. This is the default setting when you
complete a search.
Note the two additional filters for Free Full Text and HINARI
articles. These have been created in the HINARI/PubMed
searches saved in My NCBI (see module 4.5).
Of the 4849 articles, 2159 are available via the HINARI filter
and 2115 with Free full text filter ( there are some overlaps).
Note the useful options in the right column of
the PubMed search results:
Sort by Relevance (new October 2013) option
Results by year graph
Titles with your search terms listing
free full-text articles in PubMed Central (a
U.S. National Institute of Health repository)
Search details that include all fields (keyword)
AND MeSH (Medical Subject Headings)
Terms. (below those displayed)
Note the additional hypertext link for Free
article. By clicking on this link, you will be redirected to the Abstract display and be able
to access the full text.
Also note how the terms of the search –
malaria, infections and Africa - are bolded if
found in the title.
If you click on the Free Article or
Free PMC Article hyperlinks, you are
re-directed to the Abstract display.
Click on the Full text for publication
link to the publisher’s website and
the full text article.
We now will set the Display Settings drop down
menu for the Abstract Format, 20 Items per Page
and Recently Added Sort by options. To activate
these options, you will click on the Apply box.
Note the Abstract Format with 20 Items per
page and the Recently Added Sort by options
are displayed in the Display Settings line
above the abstract.
Note the Free Full Text and HINARI Filters.
We now will click on the HINARI one.
After clicking on the HINARI or Publisher’s
icon in the Abstract display, a list of all the
HINARI articles appears with the HINARI
icon. By clicking on this icon or the
publisher’s icon, the full-text article will
display. The Free Full Text filter will work in
the same way.
Note that some articles will have both the
HINARI and Free Full Text icons in the
Abstract display.
In August 2010, PubMed enhanced
the Abstract display . For ‘structured
abstracts’, the key headings
(INTRODUCTION, RESULTS,
CONCLUSIONS and KEYWORDS)
are listed at the beginning of each
paragraph. Approximately 25% of the
citations in PubMed use this format.
At the bottom of each citation, there is
the Related citations option. The results
of this search is 100 articles with 45
Free Full Text and 79 HINARI articles.
We now view the Display Settings drop
down menu for the Medline Format, 20
Items per Page and Recently Added Sort by
options. To display click on the Apply box.
Note the listing of Medical Subject Headings (MeSH)
terms in the Medline option. These MeSH terms are
assigned by the National Library of Medicine for the
indexing in PubMed. The terms can be used to
make searches broader or more precise.
We now view the Display Settings drop
down menu for the Summary Format, 200
Items per Page and Relevance Sort by
options. To activate, click on the Apply box.
Note: The relevance sort order is based on an algorithm
that analyzes each PubMed citation. For each search
query, "weight" is calculated depending on how many
search terms are found and in which fields they are found
plus a higher weight for recently-published articles.
The larger listing of 200 Citations is
useful in low-bandwidth situations.
These Summaries are Sorted by
Relevance.
We now view the Display Settings drop
down menu for the Summary Format, 20
Items per Page and Sort by Title options.
By using the Sorted by Title option, this
list of citations begins with National
Institute of Health book chapters and
then the articles are listed by title.
Another option for accessing the full-text article is
to use the PubMed ID #. In HINARI/PubMed,
enter the ID number in the search box. The
abstract version will be displayed. If this article is
a free full text or HINARI article, the icon/link will
be in the top right corner of the page.
From the Send To drop down menu, we will
be able to select the File, Collections, Order,
Clipboard, E-mail and other options.
You must place check marks in the
boxes to the left of the citations that
you wish to send to File, Collections,
Order, Clipboard and E-mail options.
If you do not place check marks in the
boxes, the entire search will be sent to
the option you choose.
From the Send To drop down menu,
we will click on File, with the Abstract
and Recently Added options. This
will be a document to be downloaded
from your Search.
Note how PubMed lists the # of
citations you have checked.
The pubmed_results has displayed as a
.txt file at the bottom of this web browser.
We will use Notepad to display the file.
Note: This file is displayed in Google
Chrome. In other web browsers, this will
display in different places.
We now view the text from a downloaded .txt
file in Notepad. You can save this file to the
C:/ drive or a flash drive or a CD-Rom.
Once saved, you can print the document.
Note: these are the citations of the articles.
Go to the HINARI Journals Collection list to
access the full-text documents.
From the Send To drop down menu,
we have selected to E-mail a file,
with the Summary and Recently
added options. This will be a
document to be sent to the e-mail
address you entered as the recipient.
In the above message, PubMed
has noted that an E-mail has
been sent to the e-mail address
you entered as the recipient.
Exercises 8-11
Complete exercises 8-11 in the workbook.
PubMed Filters
From the initial (HINARI) PubMed page,
we will run the HIV and pregnancy
search and then apply various Filters.
Note the to Advanced search and Help
options.
After completion of a search, the default
Filters are displayed in a left-column
frame. We will apply different Filters to
the results of the HIV and pregnancy
search - a total of 14236 citations.
Initially we will apply the Publication dates filter.
We have clicked on the 5 years option. This
limits the search results to 3478. Note the check
mark next to Publication Dates section. Also note
clear icon. There is a Clear all option at the
bottom of the page. If you do not clear your
options, they will be applied to future searches.
In the Specify Custom Date Range
filter, we have entered the first date of
2013 range to date (2013/01/01 to
blank) and clicked on the Apply icon.
By using a 2013 01 01 Specify Custom
Date Range filter, we have 639 citations
for HIV AND pregnancy search. Below
the results, there is the Filters activated
line that includes the Clear all option.
The specific Filters Activated is noted
with a check mark. We will click on the
Clear option to remove this . You also
can click on the specific filter.
We have cleared all the Filters and the
results of the HIV and pregnancy search
are the initial number of 14236 citations.
We have clicked on the Show
additional filters link and now
will check the Languages box
and click on Show.
Displayed is the drop down
menu for Languages filters.
Note that English is the
default language and more
than one can be checked.
We now will investigate the Article
types filters. The default types are
displayed. By clicking on more…,
you can display other options.
We have clicked on the more…
option for Article types and opened
the drop down menu. We will add
Review and Practice Guidelines
article types and click on Show.
In the Article types, we have clicked on
the Practice Guidelines and Review
options. The results of the HIV and
pregnancy search are 2301 citations.
Remember to clear these filters.
We have clicked on Show additional filters
and the drop down menu has been
displayed. We will add the Ages option by
checking the box and clicking on Show.
By clicking on more… in the Ages
filters, all the options are displayed.
For the HIV and pregnancy search, we
will check the Adolescent: 13-18 years
and Young Adult:19-24 years boxes
and click on Show. Once displayed,
we will click on the new Ages filters.
Note how the two Ages filters have
the check mark and HIV and
pregnancy search is reduced to
3534 citations. Below the results,
there is the Filters activated line
that includes the Clear all option.
We will view one final additional
set of filters by clicking the
Search fields box and Show.
A new drop down menu is
displayed. We will highlight the
Affiliation option and click on Apply.
After this filter is activated, we will
type WHO in the PubMed search
box and click on Search.
The results of the WHO affiliation
search are 6176 citations. In the
Abstract display option, we have
clicked on the Author information link.
Note the WHO affiliation of the authors.
We now will activate the journal
Search field filter, enter emerging
infectious diseases in the PubMed
search box and click on Apply.
The results of the emerging infectious
diseases journal affiliation search are
6630 citations. This search lists the
total number of articles from this
journal in PubMed. Remember to
clear this Journal search field filter.
We now will activate the Author Search
field filter, enter ribeiro in the PubMed
search box and click on Apply.
The results of the ribeiro author
search are 10530 citations. This
search lists the total number of
articles by all authors named
ribeiro in PubMed.
To further filter this search,
add the author’s initial(s). The
results of the Ribeiro e author
search are 465 citations.
The original HIV and pregnancy
search has been displayed. We will
discuss the Text availability filters.
In this example the Free full text
available filter has been activated.
The search results are 3320 citations.
This lower number does not include
any HINARI citations. Therefore, we
recommend not using these filters.
Exercise 12-15
Complete exercises 12-15 in the workbook.
Advanced Search
Advanced Search
We now will use Advanced Search
option that enables you to use the
Builder feature. Access to Advanced
Search is from the initial PubMed
page or the Search Results page.
In the Advanced Search Builder, we have
opened the All Fields drop down menu. You
can add terms in all or specific fields using
the AND, OR, NOT Boolean operators.
We have added the Text Words tuberculosis
and drug resistance to the Builder search
boxes. We have used the AND Boolean
operator. When entered, these search terms
are displayed in the box above the Builder.
Note that you can display or hide
the Index list. We have displayed
the initial list of index terms for
tuberculosis. You can enter any of
these terms into the search box.
We now will click on the MeSH
Terms option in the Builder drop
down menu and insert the term
developing countries into the search
box. We will run the Search.
The results of the tuberculosis AND drug resistance
AND developing countries search are 130 citations.
To return to Advanced Search, click on the hypertext
link below the PubMed Search box.
Note, in the Filter your results list, that there are 32
Free Full Text and 51 HINARI citations.
We have returned to the Advanced Search Builder
page. Note that the Search History has been
activated and lists the recently completed search
as #1. You can return to the Summary display of
the search results by clicking on the Items Found #.
The results of the tuberculosis AND drug resistance
AND developing countries search are 122 citations.
To return to Advanced Search, click on the hypertext
link below the PubMed Search box.
Note, in the Filter your results list, that there are 32
Free Full Text and 47 HINARI citations.
We have returned to the Advanced Search Builder
page. Note that the Search History has been
activated and lists the recently completed search
as #1. You can return to the Summary display of
the search results by clicking on the Items Found #.
Exercise 16
Complete exercises 16 in the workbook.
MY NCBI
To register , add filters and use the MY NCBI options , you
should directly access PubMed using the following address:
www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed
From the PubMed display , you will see the MY NCBI/Sign
in box. Click on this MY NCBI box to Register.
Note: if you try registering from HINARI/PubMed, HINARI
blocks you from returning after working in MY NCBI.
You will be directed to the MY NCBI
Sign In page. To register for MY NCBI,
click on the Register for an account
link. If you are already registered, you
can click on MY NCBI Sign In.
You now have to fill in a short Registration page.
Select a Username and a Password plus enter
your E-mail address. Make sure this is written
down for future reference.
You also will need to set up a Security Question
in case you forget your password.
For the 5 character image, enter this
literally including capitals. When the form
is complete, click on Create account.
Reminder: Make sure you write down
your Username and Password.
After clicking on Create account,
you will receive this message.
Go to your email account to
confirm your email address.
Open a similar confirmation email from My NCBI. Click on
the blue hypertext link to
activate the new account..
To access My NCBI, you will need to Sign In with
your Username and Password.
Note: This is the process once you have registered
and want to return to your My NCBI account.
To Sign in directly to NCBI,
enter your NCBI Username
and Password in the boxes
and click on Sign in.
After signing in to My NCBI, the PubMed
Search page will display your name and
also give you a Sign Out option. To go to
the MY NCBI page, click MY NCBI logo.
This is the MY NCBI page and includes many options that
we will discuss – 1st Filters. Filters allow My NCBI users
to identify sets of articles within search results.
Open the Filters section by clicking on the Manage Filters.
Make sure you keep the Filters for PubMed option.
In the Browse/Search for PubMed
Filters, we have clicked on Popular. The
most common filters are listed on this
page and you can choose more than 1.
When you choose a filter, the My NCBI
page will refresh and apply the filter.
By clicking on the box, choose the Free
Full Text Filter. You may choose other
filters that are of interest to you.
Note that the filter(s) you have chosen
are listed in the Your PubMed filter list
and that most recent filter added is
listed in the green box .
To add another important filter, click
on the LinkOut category.
After accessing the LinkOut
category, enter HINARI in the
search box and click on the
Search button.
Once the HINARI LinkOut option
appears, click on the Filter box to
add this 2nd filter.
Note: LinkOut is the PubMed
program that adds the HINARI icons
in the Abstract format and allows
access to the full-text documents.
Both filters you have chosen are listed in the
Your PubMed filter list. You can delete any filter
by clicking on the check in the Active column.
Return to the 1st MY NCBI page by clicking on
either MY NCBI that is next to your name or the
MY NCBI logo.
Note: these two filters are used to create
the HINARI and Free Full Text tabs that
appear when a HINARI/PubMed search is
completed. They now will appear on any
My NCBI searches that you complete.
Using the Search NCBI databases box,
complete a search for HIV AND pregnancy
- by entering the term in the search box
and clicking on Search button.
In PubMed, these are the results for the
search for HIV AND pregnancy. Click on the
Save search hyperlink that is available when
you are signed into your MY NCBI account.
My NCBI gives you the option to save or
cancel the specific search. In this case,
save the search.
By saving this search, you can receive
emails that list new citations for Free Full
Text and HINARI articles on this subject.
The green check box notes the
Save Search successful outcome.
Next, click on the Yes, please
button and Save. The following
screen will be displayed.
My NCBI has confirmed that this search was
saved. You now have the option to receive
email updates or not receive updates (about
the new articles published on this search topic).
In this case, the email updates options chosen
are: ‘Yes, please…Weekly’ on Saturday in the
Abstract format (vs. text or MEDLINE) and
receive 50 items. Select the options you want
and click on the Save button.
When you return to the My NCBI page, you can see a list of the
saved searches in the Saved Searches box - in this case ‘HIV
AND pregnancy’ and ‘malaria AND bednets’. You can re-run a
search by clicking on the title of the search. You also delete the
search by clicking on Managed Saved Searches.
Note: the email that you receive from MY NCBI will have citations
to recently published articles. To get the full-text article, you will
need to return to HINARI and locate the specific journal issue.
Notes
• We have used regular PubMed to register and
add the filters to your MY NCBI account.
• When want to make changes to your MY NCBI
profile or add/save more searches, you must go
to regular PubMed and open your MY NCBI
account. (http://www.ncbi.nlm.nih.gov/pubmed/)
• If you go to HINARI/PubMed and try to open
your MY NCBI account, you will get the
message on the next slide.
Notes continued
• The ‘saved searches’ email messages that you
receive will have the citations and abstracts but not
the links to the full-text articles.
• You will have to login to HINARI, return to the
HINARI Journal collection A-Z list, locate the
specific journal, issue and article and then view or
download the full-text.
• While your email is open, you can open a 2nd tab in
your web browser or a 2nd web browser and toggle
(go back and forth) from the email message with the
citation to HINARI.
• You also can save the citations from the email
message as a .txt or .doc and then open the file.
Additional access is from either
HINARI initial page or a Training
Materials link on the HINARI
Access the content page.
HINARI ‘Additional Resources’ Modules
• 7.1 – CINAHL Database for HINARI Users
(nursing and allied health resources)
• 7.2 – Evidence-based Practice Resources
for HINARI users
• 7.3 – WHO Resources
• 7.4 – Information Literacy
• 7.5 – E-book Recourses for HINARI users
(HINARI and Internet resources)
http://hinarigw.who.int/whalecomwww.who.int/whalecom0/hinari/training/mod
ule_7_additional_resources/en/index.html
This additional slide highlights
the Brief training HINARI Short
Course and various Training
Tools plus Presentations .
Also note the Authorship Skills
material – series of modules
written to assist researchers in
publishing their outcomes.
Exercises 17-21
• Complete exercises 17-21 in the
workbook.
• You have completed the HINARI Short
Course!
• For further instruction, go to the HINARI
Training page at
www.who.int/hinari/training/en/
Updated 2014 01