2-day workshop on Research Question & Introduction to Literature - - PowerPoint PPT Presentation

Yenepoya University-Fogarty International Center Research Ethics Master’s Program for India (NIH Grant No. 1R25 2-day workshop on Research Question & Introduction to Literature Search

We acknowledge the skills and resources provided by The Union and QMed, especially Dr Ajay MV, Dr Hemant Shewade and Ms Vasumathi Sriganesh

Story of present times……

• Where did you get this information from ??
• The Internet
• Where did you get this news from?
• Whatsapp

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Types of Research

• Qualitative vs. Quantitative
• Observational vs. Experimental
• Basic vs. Applied
• Clinical vs. population based

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• Research question vs. research interest

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Pathway of research

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Main domains of clinical research

• Therapy : medical, surgical, counselling……..
• Diagnosis:
• Prognosis :
• Harm: Unfavorable effects of therapy
• Etiology

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Types of questions

Background questions/General questions : Broad questions about the disease, condition Source: Textbooks, Review articles Foreground questions/Focussed questions: Specific questions to inform clinical decisions . Source: Medline (PUBMED), Cochrane reviews

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Some broad questions of interest

• 1. Role of cow-urine in treatment of cancer.
• 2. Role of yoga in prevention of farmer suicides.
• 3. Role of music in therapy of patients with heart disease

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Architecture of a focused question: a 4-part review question

P - Who is the patient or what problem is being addressed?

I - What is the intervention or exposure?

C – What is the comparison group? O - What is the outcome or endpoint?

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Problems with poorly focused research questions

• 1. Choice of wrong design.
• 2. Lack of clarity of protocol
• 3. Difficult to analyse and interpret results.
• 4. Difficult to publish.
• 5. Reader may not be able to interpret the answer if the

question is not clear

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Architecture of a focused question: a 4-part review question

• Patient/Problem/Population

–Disease or condition –Stage, Severity –Demographic characteristics (age, gender, etc.)

• Intervention/Index test/Input variable/exposure

–Type of intervention or exposure –Dose, duration, timing, route, etc.

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Architecture of a focused question: a 4-part review question

• Comparison/Comparator:

–Absence of risk or treatment –Placebo or Usual care –It could be internal comparison

• Outcome:

–Patient important outcomes: Both beneficial and adverse effects –Type: mortality, morbidity, quality of life, etc

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Other variations

• PECO : E= exposure .e.g. whether mobile use (E) causes brain

cancer(O)

• PEO : Effect of BP on vascular events in adults
• PO: In case there is no treatment for the condition. Or if the
• utcome is a phenomenon, perception and behaviour. Effect
• f patient admission in ICU on relatives’ feelings

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Therapy question template

In P (patients with a certain disease) what are (O) the effects (beneficial and adverse) of E (new or experimental intervention) as compared to C (control intervention)?

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Formulation of a therapy question

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Therapy question-2

Is papaya extract effective in dengue fever?

• In patients of dengue fever with severe thrombocytopenia(P)
• does administration of papaya extract(I)
• reduce the rate of bleeding (O)
• compared to placebo(C)?

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Formulation of an etiology question

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Harm Question

• In (P) patients with snake bite ,
• Does applying a tight tourniquet (E) increase the
• Risk of complications in the limb (O)

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Characteristics of a good research question:

The FINER criteria:

• Feasible: Adequate subjects, common outcomes, feasible skills,

time, money

• Interesting : Interests you, interests others(funders)
• Novel – new findings, confirms, refutes old findings, new

knowledge, may lead to innovations

• Ethical –Harm to patients? Protection of confidentiality
• Relevant : likely to have significant impact on knowledge, practice

and policy

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Where do good questions come from ??

• Observations and experiences
• Scholarship and mastering the literature.
• Being alert to new ideas and techniques
• Keeping the imagination roaming
• Choosing and working with a mentor

Hulley Stephen etal.Designing clinical research. 4th edition

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SEARCHING SCIENTIFIC LITERATURE

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POINTS TO PONDER

What do you mean by:

• Websites
• Search engines
• Databases

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What is your experience when you search:

• Online shopping websites
• Documents on web
• A name of an old friend from

school

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Understanding the needs and available resources

Examples:

• What is bioethics?
• What are the current advances in stem cell research?
• What are the available national and international guidelines
• n stem cell research?

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Understanding the needs and available resources

Examples:

• What is bioethics?
• What are the current advances in stem cell research?
• What are the available national and international guidelines
• n stem cell research?

Dictionary, Wikipedia, textbook, encyclopedia, etc Journals, theses, clinical trials reports, etc National Guidelines, guidelines from

• ther countries, NIH website, etc

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Types of resources

When we visit a website there are three types of resources:

• Type I, II and III resources
• It may a combination of some or all of these
• Textbooks are Type I resources
• Journal articles are Type II resources
• Systematic reviews are called Type III resources
• ‘Clinical Key’ is a website which has books, journals,

monographs, guidelines: Mix of all types of resources

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Important to know

• What is your need?
• Is the resource that you have selected useful or not?

KNOW YOUR RESOURCES!!

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Then ……………..INDEX MEDICUS

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AND NOW ……………..PUBMED

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Comparing Google Scholar & PubMed

Google Scholar

• It is a search engine & not

database

• It includes conference proceedings,

books, reports , etc

• Author, data, journal info accuracy

is variable

• There is no ‘tagging’ possible as it

takes it as keyword eg: ‘review’

• Search is not reproducible

PubMed

• It is a human-curated database of

journal articles

• Journals are included after a

literature review committee

• Author, title, date, journal name

entered in a uniform structured way

• Tags are possible
• Search is reproducible

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LET US ALL EXPLORE GOOGLE SCHOLAR

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What is PubMed

• Is it a search engine?
• Is it a collection of journals?
• Is it a collection of journal articles?
• Does it have only ‘English’ journal articles?

THE ANSWER TO ALL THESE IS NO

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It is an INDEX to published articles What is an INDEX? Where is it located in a textbook?

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Index

• An “index” is a resource that tells us what is published about

a topic, in one or more resources.

• A book’s index is usually found at the end of the book.

Various topics are listed alphabetically.

• Aspects of each topic may also be listed. For every topic or its

aspect, the indexer indicates in which page/s of the book we will find coverage about them.

• Eg – “Diabetic neuropathy – 59”. This means that we will find

something about diabetic neuropathy in page 59

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PubMed is an Index

• We can search and discover articles about the term or

concept we are searching for

• Result of the search includes ‘bibliographic details’
• These include: title of article, author name/s, journal,

volume, issue, page number etc.

• It has more than 27 million records in its database
• It is created and maintained by the National Library of

Medicine, located in Maryland, USA

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FOUR PRINCIPLES OF SEARCHING PUBMED:

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Principle I (Word Search)

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• There are 27.3 million records
• Each record contains words like:
• Euthanasia
• Stem cell research
• Vulnerable population
• Children
• Pregnant mothers
• Animal rights

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It only CONTAINS the word ‘vulnerable’ and ‘population

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Word search

When we search PubMed with a word or a phrase, the results contain our search It may not be about our search To make it about our search : MeSH Medical Subject Headings

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Principle II: MeSH Search

For results that are about our search terms and not ‘contain’ or search term:

• Introducing ‘tags’ that describe records
• MeSH is a ‘controlled vocabulary’ used to index articles for

MEDLINE

• Consistent way to retrieve information that may use different

terminology to describe the same concept

• If an article is indexed in MEDLINE, the MeSH term will be

assigned

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Click this

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• This article is about:
• Ethics of Biomedical Research
• History of Biomedical Research
• History of Ethics, Research
• Star or * indicates these topics

have a ‘MAJOR’ coverage

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Principle III: Field Search

Asthma IN the Title White as the Author

1302 as Page No 2015 – as Date

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Understanding the fields in PubMed

Title Author Journal name Year Volume Issue Page Perceptions of people living with HIV/AIDS regarding access to health care Vaswani V Vaswani R Med Law 2014 33 1 64-73

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Field search

With the anatomy of PubMed entry thus understood, we can instruct it to search words/number in specific fields We do this by ‘tagging’ of by using field names as follows: Social[TI] Social[tiab] Social[Jour] Social[Au] Social[MeSH] 143[page] 2016[pdat] Title Title + abstract Journal title Author List of Mesh terms Page number Date/Year

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When tagging/field searching

Remember to use:

• Square brackets []
• What you type inside is not case sensitive

Principle III: Every item in PubMed is in a structured format, and so can be represented in a structured format like a table. We can search for our search term in specific parts of the record

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Principle IV: Boolean Operators

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Using Boolean Operators

• If I want to find records in PubMed for BOTH:
• 1. Articles in medical ethics
• 2. Articles in nursing ethics

Can I search: medical ethics and nursing ethics? Try and search this way and note the numbers that you get About 4500…………..?

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• Now try this:

medical ethics[mesh] AND nursing ethics[mesh]

• Also note the changes in

the ‘search details’ box on the right side

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Boolean operators

They are the prepositions/conjunctions in the language of PubMed AND OR NOT All in capitals i.e. it is case sensitive

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Using Boolean operators

Results in PubMed CONTAINING these: 4505 Results in PubMed ABOUT these: 420 Results in PubMed >5500 The records are about minimum one term Results are about medical ethics but NOT nursing ethics

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Another example:

Records containing Asthma

10

Records containing Bronchitis

7

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Asthma AND Bronchitis

Records containing Asthma

10

Records containing Bronchitis

7

4

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Asthma OR Bronchitis

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Asthma NOT Bronchitis

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Principle IV

When searching for two or more terms, use ‘Boolean

• perators’

AND Results contain terms together, there are less results OR Results contain at least one term of the both, there will be more results NOT Results contain the first term, and do not contain the rest , less results

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Quick recap and exercises

I want to read up articles by Prof Ruth Faden on social justice Faden, Ruth[Au] AND social justice[MeSH] I want to read up articles by her from journal of medical ethics Faden, Ruth[Au] AND Journal of Medical Ethics [jour]

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I need to quickly read something about professionalism and social justice professionalism[ti] AND social justice[ti] Search results: only 4 professionalism[tiab] AND social justice[tiab] Search results: 49

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SEARCHING WITH MESH TERMS

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MeSH..ing around……….

• MeSH is the controlled vocabulary used to index

articles for MEDLINE.

• It provides a consistent way to retrieve information

that may use different terminology to describe the same concept.

• If an article is indexed for MEDLINE the MeSH terms

will be assigned as keywords to each of the indexed articles.

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MeSH..ing around……….

• If we search for articles using MeSH headings alone, you will

find only those articles that have been indexed for MeSH terms.

• We will miss those articles that are PubMed, but not indexed

for MEDLINE, as they will not have MeSH terms assigned to their records.

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Exploring the Mesh Data base

• Two ways to access it:

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Where do these MeSH come from? What are they?

• Trained indexers analyze the content of the articles
• They assign MeSH terms and subheadings
• Arranged in a hierarchical manner called MeSH Tree

Structure

• It is updated annually

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Understanding the Anatomy of MeSH

Lets try and search: ‘professionalism’

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Understanding the Anatomy of MeSH

Scope Note

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Understanding MeSH terminologies

MeSH vocabulary:

• 1. Scope Note
• 2. Subheadings
• 3. Entry terms
• 4. MeSH tree
• 5. Option to restrict to major topic
• 6. Options for MeSH tree restriction

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MeSH Vocabulary

• MeSH headings: Scope Note
• It is just below the term we

chose

• Tells us the meaning of the term
• It also gives useful information
• f what other MeSH terms that

describe the condition, what the indexers would not include, etc

• Useful to read the scope note

when doing a focused research

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Scope Note: some unique examples

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MeSH Vocabulary

• MeSH Subheadings
• Describe a specific aspect of a

concept

• When we view a MeSH term, we
• nly see subheading applicable

to that MeSH term

• Eg: For Bioethics
• Education
• History
• Organization and administration
• trends

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MeSH Vocabulary: Subheadings

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MeSH Vocabulary

• MeSH Entry Terms
• These are synonyms, alternate

forms and other closely related terms

• These are generally used

interchangeably

• Eg: For Bioethics
• Health Care Ethics,
• Ethics, Health Care
• Biomedical Ethics

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Understanding MeSH: Hierarchy/Tree

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MeSH Tree

• From broad to narrow terms like

branches of a tree

• Lower terms become more

specific

• Sometimes it may not have

lower terms

• Differentiate it with subheadings

which are aspects of a MeSH term

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MeSH: Restrict to Major Topic

• When we choose a MeSH term

and search, it automatically includes a search of all the lower terms

• Check: Restrict to MeSH Major

topic

• It will include articles where the

article is majorly about it

• It will have star * in the MeSH

terms below the abstract

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Restrict to major & Do not include MeSH below this term

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Recap

We just learned:

• The MeSH terms
• Subheadings
• Entry terms
• MeSH tree
• Restrict to major option
• Do not include MeSH terms found below this term in MeSH

hierarchy

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Hands On exercises

Do the following searches:

• 1. History of human rights
• 2. Focused search on history of human rights
• 3. Human rights: general articles, not the more specific types
• f child rights, patient rights, etc

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Building search using MeSH

The PubMed search box here

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Using the MeSH search box

• Search one term at a time
• Add each term to the search builder
• Search PubMed after building the search
• One can also choose subheadings under the MeSH term

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PUBMED: Narrowing or Focusing Search

Let us explore the following:

• Understanding the available filters
• Applying filters
• Applying filters with Boolean operators
• Single citation matcher page

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Scope of filters

• By default two types of articles are available
• Clinical trials and review
• You can even customize
• Click and explore the customize option

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Scope of filters

• Abstract: the results will contain only those

that have an abstract

• Free full text: what does it mean
• Full text: Free as well non-free full text
• Everytime you apply the filter, note the

changes that occur in the search box

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Scope of filters

• Filter by dates helps in further narrowing
• Explore the customize range
• Combines the search with AND

humans[mesh]

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Scope of filters

• Languages: PubMed has articles in other

languages other than English

• Sex
• Subjects: It has nine different subjects
• Journal categories: helps in finding nursing,

dental journals and core clinical journals

• Ages

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PubMed: Display Formats

• The default display when we search is the ‘Summary format’
• The results are shown in the order of ‘Most Recent’
• There will be 20 results per page
• All these can be changed

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CREATING MY NCBI ACCOUNT AND SAVING SEARCH STRATEGIES AND SEARCH RESULTS

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• Go to PubMed – www.pubmed.gov
• Click Sign in to NCBI

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• If you have a gmail / google account,

click “sign in with google” and follow steps to register

• If not, click “Register for an NCBI

Account” and create your account

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Steps for My NCBI Account

• Choose “Sign in with google”
• Enter your gmail / google login

and password

• In the next screen click ‘accept’
• In the next screen click ‘Create a

new NCBI account’ and click ‘continue’.

• In 5 second the page will

automatically redirect to the PubMed Home page.

• Click – ‘Register for an NCBI

account’

• Fill in all details and create your

account

• (Look out for any message that

says your user name is already taken)

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Setting Preferences

• Under Common Preferences

– Click Highlighting – Choose a colour – Click Save (at the end of the page)

• Click the Back button to go to the PubMed Home Page

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Saving Search Strategies

Demonstration: ("Nursing Care"[Mesh]) AND "Bioethics"[Mesh]

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Saving Search Strategy

• We got 58 search results
• Click create alert just below the search box
• In the next page: choices are available
• By default the name of the search will be search strategy
• You can change it to more meaningful title

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Type meaningful title here You can even receive email alerts You can choose the format of your search results with or without abstracts, HTML, etc Number you want to receive

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Saving Search results

• The options available are:
• Emails
• File if you want it saved in your computer
• Clipboard allows temporary storage

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• Summary: same as it appears in

default PubMed search

• Abstract: along with abstracts
• MEDLINE format: Reference

management

• XML format if to be taken to a

website

• PMID list
• CSV format: to bring it to Excel

format

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• If large number of results you

can use the check boxes

• If you copy to clip board: next

page with show the message: copied to clip board

• You can even remove from clip

board

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• You may choose to add it

your NCBI account

• Click on Collections
• Next: Add to collections
• Here the page is

redirected

• If it is a new collection,

‘create new collection’

• Save
• Access any time from My

NCBI

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Managing collection

• Collections are on the right lower corner
• As you create more collections, you may delete the old ones

that are not required

• Manage collection offers merging and deleting options

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Saving search results: Email

• Choosing display format
• Sort order
• Number of items: Max is 200
• Start from citation: this option is

because it allows only 200 items

• So the next batch of items can

be from 201

• You make the subject more

readable

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• Option ‘Order’ not very usefult

in India, but in US you can order through the libraries

• My Bibliography: to save your
• wn publications

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Explore the Single Citation Matcher

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Exercises for Single Citation Matcher

Search the following:

• 1. Articles by Dr Anant Bhan on trials
• 2. Article on publication ethics in Indian Journal of Medical

Ethics

• 3. Articles on publication ethics in 2017
• 4. Indian journal of ophthalmology: 2017 Jun; 65(6)

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PubMed Advanced Search

If we choose to add MeSH terms or entry terms and use Boolean Operators

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Exercise and Demonstration

Building search using a research question RQ: What is the treatment outcome patients with tuberculosis and diabetes? Tease out the following:

• Important concepts
• MeSH terms
• Text words
• Make a table for ready reference at later date

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Concept MeSH terms Text words (can copy paste entry terms)

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Concept MeSH terms Text words (can copy paste entry terms)

tuberculosis Tuberculosis[MeSH] Tuberculosis TB Koch’s disease diabetes Diabetes Mellitus[mesh] Diabetes Mellitus DM Hyperglycemia Hyperglycaemia High blood sugar Treatment

• utcomes

Treatment

• utcome[mesh]

Death[mesh] Treatment outcome Loss to follow-up Death Clinical effectiveness* Patient relevant outcome* *means truncation and can have things such as clinical effectivenesses

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Hands-on practice

Exercise: We need to find articles by Prof Ruth Faden in the field of women’s health

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To Sum up

• Focused research question
• Identifying PICO
• Identifying MeSH terms
• Searching efficiently in PubMed
• Single citation matcher
• Advance builder
• Saving searches in various ways

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HAPPY SEARCHING