Transcript Document

About the papers
Bin Liu (刘滨), PhD, Associate Professor
Intelligent Computing Research Center
Homepage: http://bioinformatics.hitsz.edu.cn/
Email: [email protected] or [email protected]
Course web site
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http://bioinformatics.hitsz.edu.cn/course/
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Course information, PPT, papers, books,
project information can be found on this
web site.
Thank Junjie Chen for constructing this web site
http://bioinformatics.hitsz.edu.cn/course/
As a master, when you do
research on a given topic,
you would ask….
What should I do?
What did other researchers do?
How did they do?
Medical Literature retrieval
Importance：
 Literature is an important tool for storing
techniques and knowledge, which is very
important for research
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Literature is a measure of researchers.
1、retrieval methods：
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（1）trace back
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（2）search engine
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（3）Journal website
Pubmed
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PubMed is a free database accessing primarily
the MEDLINE database of references and
abstracts on life sciences and biomedical topics.
PubMed is NCBI gateway to MEDLINE
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including more than 4600 medical journals
http://www.ncbi.nlm.nih.gov/pubmed
Alcoholic AND disease
Advanced search
history
"Liu Bin" AND ("Harbin Institute of Technology Shenzhen Graduate
School”)
Other database
Elsevier、Springer、Wiley InterScience、
BMC、Plos、WorldSciNet、Bentham
Science、Oxford、Nature、Physical
Review、Blackwell Synergy、Libertas
Academica、CNKI、万方、维普
1. Elsevier
Elsevier publishes 250,000 articles a year in
2,000 journals.[1] Its archives contain seven
million publications. Total yearly downloads
amount to 240 million.
http://www.sciencedirect.com/
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Bioinformatics journals in Elsevier
Journal
IF
Cell
31.253
Trends in Genetics
8.659
Journal of Molecular Biology
4.146
Biochemical and Biophysical Research Communications 2.648
FEBS Letters
3.264
Journal of Theoretical Biology
2.454
Gene
2.578
Computational Biology and Chemistry
1.837
Biophysical Journal
4.683
Bioinformatics journals in Springer
Journal
IF
Amino Acids
4.132
Journal of Human Genetics
2.431
Mammalian Genome
2.35
Acta Biotheoretica
0.735
Journal of Mathematical Biology
1.577
Journal of Biosciences
1.703
Chromosome Research
3.405
Journal of Molecular Modeling
2.018
http://scholar.google.com/
3. 中国知网
http://edu.cnki.net/
目前期刊总计9357种，1157300期，共计文章36753208篇。
http://www.dlib.cnki.net/kns50/
尧德中
Wiley InterScience:
http://www3.interscience.wiley.com/cgibin/home
BMC: open access (OA)
http://www.biomedcentral.com/home/
PloS: (OA)
http://www.plos.org/
WorldSciNet:
http://www.worldscinet.com/
Bentham Science:
http://www.bentham.org/
Oxford:
http://www.oxfordjournals.org/
Nature:
http://www.nature.com/
Other Bioinformatics Journals
Journal
Bioinformatics
Nucleic Acids Research
Briefings in Bioinformatics
Molecular Biology and Evolution
DNA Research
BMC Genomics
BMC Bioinformatics
Genome Biology
PLoS Computational Biology
PLoS ONE
IF
4.328
6.878
4.627
7.28
3.612
3.926
3.781
6.153
5.895
4.092
Journal
Journal of Computational Biology
IF
Biopolymers
1.563
10.176
9.38
3.419
3.39
2.823
Nature
42.351
Science
31.477
生物化学与生物物理进展
SCIE
生物物理学报
核心
生物信息学
核心
Genome Research
P NATL ACAD SCI USA（PNAS）
Proteins
Journal of Computational Chemistry
Biology Letters
Comparative and Functional
Genomics
Genes & Development
Journal of biomolecular
structure and dynamics
Molecular & Cellular
Proteomics
Molecular BioSystems
Journal of Proteome
Research
Protein & Peptide Letters
The European Physical Journal
E
Molecular Microbiology
Current Bioinformatics
BMC Systems Biology
Current Protein & Peptide
Science
Analytical Biochemistry
proteomics
Physical Review E
How to access papers
Pubmed
 Journal website
 Google
 VPN
 BBS
 Friends
 authors
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Reference management
Reference management software
Reference Manager
 Endnote
 ProCite
 BibTeX
 RefWorks
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advantages?
as a database
 Format
 easy insert and delete
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How to measure the quality of journal
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Impact factor
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The impact factor (IF) of an academic journal is a
measure reflecting the average number of citations to
recent articles published in that journal. It is frequently
used as a proxy for the relative importance of a journal
within its field, with journals with higher impact factors
deemed to be more important than those with lower
ones. The impact factor was devised by Eugene Garfield,
the founder of the Institute for Scientific Information.
Impact factors are calculated yearly starting from 1975
for those journals that are indexed in the Journal
Citation Reports.
How to rate a researcher
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h-index
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The h-index is an index that attempts to
measure both the productivity and impact of
the published work of a scientist or scholar.
The index is based on the set of the scientist's
most cited papers and the number of citations
that they have received in other publications.
h-index in Google Scholar
How to Read a Scientific Paper
Key Topics
Types of scientific papers
 Organization of a paper
 Actions to take – to properly read a paper
 Difficulties in reading scientific papers
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Types of Scientific Papers
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Original article – information based on original research
Application notes - describe a specific technique or
procedure
Review – detailed analysis of recent research on a specific
topic
Editorial – often short review or critique of original articles
Letter to the Editor – short & on subject of interest to readers
Effective Medical Writing. Peh WCG &, NG K H Singapore Medical Journal
2008 49(7) 522 smj.sma.org.sg/4907/4907emw1.pdf (accessed 05
November 2013)
Organization of a Paper
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Abstract
Introduction
Methods
Results
Discussion/Conclusions
Acknowledgements
References
Note: most scientific journals follow the format of the
Structured Abstract. Occasionally, the Results and
Discussion are combined – when the data need
extensive discussion to allow the reader to follow
the train of logic of the research.
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Abstract - a summary (~ 150-200 words) of the
problem, the method, the results and the
conclusions; the reader can decide whether or
not to read the whole article
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Introduction - clearly states the problem being
investigated & reasons for the research;
summarizes relevant research to provide context;
identifies the questions being answered; briefly
describes the experiment, hypothesis(es),
research question(s) & general experimental
design or method
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Methods - provides the reader enough details
so they can understand and replicate the
research; explains how the problem was studied;
identifies the procedures followed; explains new
methodology in detail; includes the frequency of
observations, what types of data were recorded,
etc.
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Results - presents the findings, and explains
what was found; shows how the new results are
contributing to the body of scientific knowledge;
follows a logical sequence based on the tables
and figures presenting the findings to answer the
question or hypothesis(es)
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Discussion/Conclusions - describes what the
results mean regarding what was already known
about the subject; indicates how the results
relate to expectations and to the literature
previously cited; explains how the research has
moved the body of scientific knowledge forward;
outlines the next steps for further study
Acknowledgements – recognize various
contributions of other workers
References - the sources of previously
published work; includes information not from
the experiment and not ‘common knowledge’
Actions to Take
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Skim the article without taking notes:
 Read the abstract; it will tell you the major
findings of the article and why they matter
 Read first for the ‘big picture’
 Note any terms or techniques you need to define
 Jot down any questions or parts you don’t
understand
 If you are unfamiliar with any of the key concepts
in the article, look them up in a textbook
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Re-read the article more carefully especially the
‘methods’ and ‘results/conclusions’ sections:
 Carefully examine the graphs, tables, and
diagrams
 Try to interpret the data first before reading the
captions and details
 Make sure you understand the article fully
Ask yourself questions about the study, such as:
 What problems does the study address? Why is
it important? Is the method good? Are the
findings supported by evidence? Are they unique
and supported by other work in the field?
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Write a ‘summary’ of the article
 Describe the article in your own words, write down
the sentences can be used in your own papers in
the future (important for Chinese students)
 Note the ‘key points’ - purpose of the study/questions
asked, assumptions, major findings & conclusions,
questions unanswered & any surprises
How to Read and Review a Scientific Journal Article Duke University
Writing Studio
twp.duke.edu/uploads/media_items/scientificarticlereview.original.pdf
(accessed 05 November 2013)
Other Useful Hints
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Draw inferences (a conclusion reached on the basis of
evidence and reasoning):
 not everything in an article is stated explicitly; rely on
your prior knowledge/experience and the background
in the article, to draw inferences from the material
Distinguish main points:
 Document level: in title, abstract and keywords
 Paragraph level: look for words/phrases like
unexpected, in contrast to previous work,
hypothesize that, propose, introduce, data suggests
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Take notes as you read:
 this improves recall and comprehension; you may
think you’ll remember everything but details will
slip away
 develop a template for recording notes on articles
 can use the structured abstract format (abstract,
introduction, methods, results, discussion &
conclusions, references)
How to read a scientific article: Mary Purugganan & Jan Hewitt,
Rice University
www.owlnet.rice.edu/~cainproj/courses/HowToReadSciArticle.pd
f (accessed 05 November 2013)
Difficulties in Reading Papers
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Papers can be poorly written
Bad writing has consequences for the reader
The reader cannot easily understand what the
experiment was
Lack background information or training
Additional Resources
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Effective Medical Writing. Peh WCG &, NG K H
Singapore Medical Journal 2008 49(7) 522
smj.sma.org.sg/4907/4907emw1.pdf
How to read a scientific article. Mary Purugganan & Jan
Hewitt, Rice University
www.owlnet.rice.edu/~cainproj/courses/HowToReadSciAr
ticle.pdf
How to read a scientific paper. John W. Little & Roy
Parker--University of Arizona
www.biochem.arizona.edu/classes/bioc568/papers.htm
How to read and review a scientific journal article. Duke
University Writing Studio
twp.duke.edu/uploads/media_items/scientificarticlereview.
original.pdf