How to Read a Paper and Survey Literature

P Sunthar

Department of Chemical Engineering

Indian Institute of Technology, Bombay
Mumbai 400076, India
P.Sunthar@iitb.ac.in

February 3, 2014
 Organisation Three Passes Literature References

Recall: Essence of Tech. Comm.

Question
Research Problem: What to find ?

Answer
Precise answer to the question, of what was found.

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 Organisation Three Passes Literature References

Recall: Sci. Method and Comm.

Observation Communicate

Question
The Scientific Method

Y
Literature Hypothesis 1 Prediction 1 Test 1 ? Communicate

Y
Literature Hypothesis 2 Prediction 2 Test 2 ? Communicate

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 Organisation Three Passes Literature References

Outline of the Lecture

1 Organisation of Scientific Literature

2 Three Pass Approach

3 Literature Survey

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 Organisation Three Passes Literature References

Types of Scientific Literature

Journal Articles (Letter, Original, Review)

Patents
Monographs
Handbooks/Encyclopedias
Textbook

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 Organisation Three Passes Literature References

Journal Article or Paper

Title: Short sentence for key contribution

Author and Affiliation
Abstract
Introduction
Literature Survey
Methods (Experimental or Theoretical)
Results and Discussion
Conclusion
References

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 Organisation Three Passes Literature References

First Pass Read (Observe)

The Three passes, Adapted from Keshav [2007]

1 Observe, 5–15 mins
2 Judge, 10–15 mins
3 Understand, few hours
The First Pass
Read Title, Abstract, and Introduction
Browse through section headings, skip contents
Read Conclusions

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 Organisation Three Passes Literature References

First Pass Notes

Note the following points
Bibliographic details (underline communicating author)
Type of article: Letter, Original, Review
Nature of the work: Expt., Comp. Simul., Theory
DOI: http://dx.doi.org/ 10.1038/nature11311
Digital Object Identifier: Persistent URLs for online
documents
Broad area: Look for keywords in title and abstract
What is the main question addressed?
What is the answer provided?
New observation reported ?
Is a new hypothesis being proposed ?
Existing hypothesis being tested on a new system ?
First pass should not be critical, just note down objectively.
Summarise in less than 30 words.
Should take from 5 to 15 minutes
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 Organisation Three Passes Literature References

First Pass Notes

Note the following points
Bibliographic details (underline communicating author)
Type of article: Letter, Original, Review
Nature of the work: Expt., Comp. Simul., Theory
DOI: http://dx.doi.org/ 10.1038/nature11311
Digital Object Identifier: Persistent URLs for online
documents
Broad area: Look for keywords in title and abstract
What is the main question addressed?
What is the answer provided?
New observation reported ?
Is a new hypothesis being proposed ?
Existing hypothesis being tested on a new system ?
First pass should not be critical, just note down objectively.
Summarise in less than 30 words.
Should take from 5 to 15 minutes
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 8 / 28
 Organisation Three Passes Literature References

First Pass Notes

Note the following points
Bibliographic details (underline communicating author)
Type of article: Letter, Original, Review
Nature of the work: Expt., Comp. Simul., Theory
DOI: http://dx.doi.org/ 10.1038/nature11311
Digital Object Identifier: Persistent URLs for online
documents
Broad area: Look for keywords in title and abstract
What is the main question addressed?
What is the answer provided?
New observation reported ?
Is a new hypothesis being proposed ?
Existing hypothesis being tested on a new system ?
First pass should not be critical, just note down objectively.
Summarise in less than 30 words.
Should take from 5 to 15 minutes
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 8 / 28
 Organisation Three Passes Literature References

First Pass Notes

Note the following points
Bibliographic details (underline communicating author)
Type of article: Letter, Original, Review
Nature of the work: Expt., Comp. Simul., Theory
DOI: http://dx.doi.org/ 10.1038/nature11311
Digital Object Identifier: Persistent URLs for online
documents
Broad area: Look for keywords in title and abstract
What is the main question addressed?
What is the answer provided?
New observation reported ?
Is a new hypothesis being proposed ?
Existing hypothesis being tested on a new system ?
First pass should not be critical, just note down objectively.
Summarise in less than 30 words.
Should take from 5 to 15 minutes
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 8 / 28
 Organisation Three Passes Literature References

First Pass Notes

Note the following points
Bibliographic details (underline communicating author)
Type of article: Letter, Original, Review
Nature of the work: Expt., Comp. Simul., Theory
DOI: http://dx.doi.org/ 10.1038/nature11311
Digital Object Identifier: Persistent URLs for online
documents
Broad area: Look for keywords in title and abstract
What is the main question addressed?
What is the answer provided?
New observation reported ?
Is a new hypothesis being proposed ?
Existing hypothesis being tested on a new system ?
First pass should not be critical, just note down objectively.
Summarise in less than 30 words.
Should take from 5 to 15 minutes
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 Organisation Three Passes Literature References

Organisation of a Paper

Observation

Significance

Problem

Result

Broder Implication

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 Organisation Three Passes Literature References

Clarity of a Question
Problem
Topic : Name/Area/Title
Question : Who/What/Where/When/Why/How ?
Practical or Conceptual Significance : So What ? For
understanding What ?
1 The authors have studied (topic)
2 because they wanted to find out
(why/what/how)
3 in order to understand (significance)
The authors have studied Martian landscapes because they
wanted to find out what some dark markings on the surface
images were, in order to understand the surface chemistry and
physics.
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 10 / 28
 Organisation Three Passes Literature References

Clarity of a Question
Problem
Topic : Name/Area/Title
Question : Who/What/Where/When/Why/How ?
Practical or Conceptual Significance : So What ? For
understanding What ?
1 The authors have studied (topic)
2 because they wanted to find out
(why/what/how)
3 in order to understand (significance)
The authors have studied Martian landscapes because they
wanted to find out what some dark markings on the surface
images were, in order to understand the surface chemistry and
physics.
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 10 / 28
 Organisation Three Passes Literature References

Clarity of a Question
Problem
Topic : Name/Area/Title
Question : Who/What/Where/When/Why/How ?
Practical or Conceptual Significance : So What ? For
understanding What ?
1 The authors have studied (topic)
2 because they wanted to find out
(why/what/how)
3 in order to understand (significance)
The authors have studied Martian landscapes because they
wanted to find out what some dark markings on the surface
images were, in order to understand the surface chemistry and
physics.
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 10 / 28
 Organisation Three Passes Literature References

Clarity of an Answer

Arguments in a Solution [Booth et al., 2008]

Claim or Thesis
Reason : What reasons support the claim ?
Evidence : What evidence supports the reasons ?
1 The author claims that
2 because of (reason/principle)
3 which is based on (material evidence).
The authors claim that the marks are due to liquid brine flows
because the patterns appear to be seasonal between
liquid-like-flow and solid like frozen state, which is based on
the surface temperatures and possible occurrence of salts which
can absorb water on the surface.

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 Organisation Three Passes Literature References

Clarity of an Answer

Arguments in a Solution [Booth et al., 2008]

Claim or Thesis
Reason : What reasons support the claim ?
Evidence : What evidence supports the reasons ?
1 The author claims that
2 because of (reason/principle)
3 which is based on (material evidence).
The authors claim that the marks are due to liquid brine flows
because the patterns appear to be seasonal between
liquid-like-flow and solid like frozen state, which is based on
the surface temperatures and possible occurrence of salts which
can absorb water on the surface.

P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 11 / 28
 Organisation Three Passes Literature References

Clarity of an Answer

Arguments in a Solution [Booth et al., 2008]

Claim or Thesis
Reason : What reasons support the claim ?
Evidence : What evidence supports the reasons ?
1 The author claims that
2 because of (reason/principle)
3 which is based on (material evidence).
The authors claim that the marks are due to liquid brine flows
because the patterns appear to be seasonal between
liquid-like-flow and solid like frozen state, which is based on
the surface temperatures and possible occurrence of salts which
can absorb water on the surface.

P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 11 / 28
 Organisation Three Passes Literature References

Memorise This!

Question
TQS: Topic, Question, Significance

Answer
CRE: Claim, Reason, Evidence

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 Organisation Three Passes Literature References

Second Pass: Judgemental

Look at Figures and Illustrations

Graphs have error bars (statistically significant conclusion)
Axis properly marked (not shoddy or casual reporting)
Figures are neatly drawn
Is the problem stated clearly ?
Is the solution properly justified.
Is the methodology adopted appropriate ?
Has the author published similar work (look for references
and citations in Scopus) ?
Confidence in authors experience
Incremental embellishments may not be significant
Note down your judgements, including the problem
statement and thesis in your own words.
Should take another 15 minutes.

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 Organisation Three Passes Literature References

Third Pass: Understanding

Understanding and Reviewing

Read methodology carefully
Read relevant literature (cited refs and books)
Read every sentence critically, challenging the
assumptions made
Mental Recreation of work
If you were to repeat how would you have proceeded
Verify mathematical proofs, where possible.
Brings more clarity and insights
Presents ideas for alternate approaches and extensions
Are there any missed literature

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 Organisation Three Passes Literature References

Critically Reviewing a Paper

After first or second pass:
1 Write down the overall purpose as you see it: Problem and
Thesis
2 Does the introduction establish this ?
3 Body of the Work
1 Is the paper focussed on this goal?
2 Are the reasons (and assumptions) that justify the claim
valid ?
3 Are there sufficient and reliable evidence to support the
reasons?
4 Conclusion: Is it strong finish or simply a weak summary
of the paper?
5 Check the grammar and spelling, and note down typos.
6 Examine the citations (completeness, correctness, and
formatting style)
7 Your final comment: Are you convinced by the reasoning
and the evidence ?
P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 15 / 28
 Organisation Three Passes Literature References

Critically Reviewing a Paper

After first or second pass:
1 Write down the overall purpose as you see it: Problem and
Thesis
2 Does the introduction establish this ?
3 Body of the Work
1 Is the paper focussed on this goal?
2 Are the reasons (and assumptions) that justify the claim
valid ?
3 Are there sufficient and reliable evidence to support the
reasons?
4 Conclusion: Is it strong finish or simply a weak summary
of the paper?
5 Check the grammar and spelling, and note down typos.
6 Examine the citations (completeness, correctness, and
formatting style)
7 Your final comment: Are you convinced by the reasoning
and the evidence ?
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 Organisation Three Passes Literature References

Reading Nature Articles

Nature/Science Podcasts
News and Views
Read the actual article

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 Organisation Three Passes Literature References

Reading Skills and Communication Skills

Is reading skill a Communication Skill

What communication skills can you improve by having a
good reading skill ?
How can you improve your Communication Skills, with
this?

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 Organisation Three Passes Literature References

Reading Skills and Communication Skills

Is reading skill a Communication Skill

What communication skills can you improve by having a
good reading skill ?
How can you improve your Communication Skills, with
this?

P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 17 / 28
 Organisation Three Passes Literature References

Reading Skills and Communication Skills

Is reading skill a Communication Skill

What communication skills can you improve by having a
good reading skill ?
How can you improve your Communication Skills, with
this?

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 Organisation Three Passes Literature References

Searching for Literature I

Starting Points
Keywords Search
Problem description statement
Article/Report given to you
Author search
Advisor: Ask, Validate your list
Search Resources
SCOPUS (for general search)
ISI Web of Knowledge and Citebase (citation searches)
Engineering Village Compendex and Inspec (general
search)
Google Scholar, Yahoo Mindset (for web search of scholarly
articles)
Patents search (Google, Free-Patents, Scopus Patents Tab)
Wikipedia, Google, may be used to get broad ideas but
cannot yet be considered authoritative search.

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 Organisation Three Passes Literature References

Searching for Literature II

Review Journals Search

Annual Review series
Advances series
Reviews of . . . series

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 Organisation Three Passes Literature References

Citation Based Search

References and Citations
References: Related work done earlier
Citations: Related work done afterwards
Year

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 Organisation Three Passes Literature References

Citation Tree: Related Literature

Given Bibliographic Entry
Reference articles cited by this article , (call it parents)
Citations have referred to this article , (call it children)
Related articles have common ancestory (call it cousins)
Year

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 Organisation Three Passes Literature References

Important Work and Review Paper

Year

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 Organisation Three Passes Literature References

Keyword vs Citation Search

Keyword Based Citation Based

Best when no relevant article is Best when highly relevant arti-
known cle is known
Wrong keywords =⇒ consid- Related articles found instantly,
erable delay mostly relevant
Chances of missing an impor- ancestory chain of relations
tant work could be high shows important work
prior experience for good start- Only one article required
ing guess
Each survey is freshly done Builds upon the literature sur-
vey done by others
Easy to manage initially Can get messy to manage

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 Organisation Three Passes Literature References

Taking Electronic Notes

During first and second pass:

1 Highlight important sentences in PDF (use Acrobat,
PDF-Xchange viewer or android and Apple apps on a
tablet)
2 Take notes on a word processing software (Google Docs,
LibreOffice, Word)
3 Organise by Topic and Ascending year of publication
4 Write down the downloaded file name, DOI
5 Cut and paste highlighted sentences
6 All notes in one place. Helpful in analysing literature

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 Organisation Three Passes Literature References

Electronic Notes Sample

Author citation
Filename

DOI

Topic
Notes

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 Organisation Three Passes Literature References

Naming a PDF File

1 Key information: Year, keywords

2 Unique name
3 Sample syntax: YYYYjabrevPPP-keywords.pdf
4 Example: 1999cocis33-lipid-origin-luisi.pdf
5 cocis: Current Opinion in Colloidal and Interface Science
6 Year=1999 and Page=33 usually uniquely identifies a
paper in a given journal
7 Unique file name helps in removing Duplicates
8 Alternatively use: www.Mendeley.com (organising
bibliographic information and PDF files, share in a group)

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 Organisation Three Passes Literature References

Naming a PDF File

1 Key information: Year, keywords

2 Unique name
3 Sample syntax: YYYYjabrevPPP-keywords.pdf
4 Example: 1999cocis33-lipid-origin-luisi.pdf
5 cocis: Current Opinion in Colloidal and Interface Science
6 Year=1999 and Page=33 usually uniquely identifies a
paper in a given journal
7 Unique file name helps in removing Duplicates
8 Alternatively use: www.Mendeley.com (organising
bibliographic information and PDF files, share in a group)

P Sunthar (IIT Bombay) How to Read a Paper and Survey Literature February 3, 2014 26 / 28
 Organisation Three Passes Literature References

Organising Literature: Traditional Method

Use a separate hardbound book.

Serially number the articles as you get them
Include bibliographic info
Summarise your first pass read notes.
Categorise (last section of the book)
1 Put numbers (labels) under categories
Use categories as starting point of writing report

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 Organisation Three Passes Literature References

Bibliography

S Keshav. How to read a paper. ACM SIGCOMM Comp.

Commun. Rev., 37:83–84, 2007.
Wayne C. Booth, Gregory G. Colomb, and Joseph M. Williams.
The Craft of Research. The University of Chicago Press, 3
edition, 2008.

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