Literature Search Course 2013 - ETH Zn.ethz.ch/~nielssi/download/4. Semester/Praktikum GL der...

Literature Search Course 2013

Friday 15.3. / 26.4. / 24.5.2013 – HG E 27 contact in case: fuhrer@imsb.biol.ethz.ch

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Time Program

9:00 – 10:00 Introduction

10.00 – 10.15 Break

10.15 – 12:00 Literature databases and searches

12:00 – 13:00 Lunch break

13:00 – 14:30 Reference Management, Alerts and Copyright

14:30 – ~17.00 Final Exercise (Breaks on your own)

Introduction

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What is Scientific Literature?

• All scientific information published in specialized journals, books and any other media.

• Represents the current knowledge in a particular scientific field at that time.

• Evolves at the speed of journal, book, and abstract publications (online and paper).

• Collected in databases accessible on the internet and in libraries (and labs…).

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Why Conduct a Literature Search?

• for designing new research projects

• for keeping track of the most recent developments in the field

• for getting technical information

• for writing a scientific report/paper

• for tracking other scientists’ research direction

Many Different Types of Publications

• General articles: basic information about a topic, accessible to scientists and non-scientists (e.g. text books, supermarket magazines, newspapers, etc.)

• Research articles: latest findings in a specific field with original data

• Review articles: a summary of research articles and hypotheses on a particular topic conducted up to that point in time

• Book articles: review or research reports included in book chapters

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Many Different Focus of Journals

• Journals for all fields of science.

Nature, Science, Cell, PNAS (Proceedings of the National Academy of Sciences), PLoS (Public Library of Science), ...

• Specialized journals

Blood, Journal of Molecular Biology, Acta Cryst., Proteins, Bioinformatics, Molecular & Cellular Proteomics, ...

• Review journals

Current Opinion, Annual Reviews, Nature Reviews, ...

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Literature business / characteristics • Peer Review

Prior to publication the manuscript is reviewed by experts in the same field

• Impact factor Average number of citations per article in a journal over some time period (usually 2 years)

• Open access journals Articles are available online to readers without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself.*

BioMed Central collection, PLoS collection

• License Ask journals for permission for printing figures or charts from other articles.

* http://en.wikipedia.org/wiki/Open_access_journal

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Structure of a Scientific Publication

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Structure of a Scientific Publication

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Structure of a Scientific Publication

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Structure of a Scientific Publication

Literature databases and searches

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Relevant literature databases

• Amount of electronically available information is vast. • Currently about ~21’000 “peer-reviewed” journals.

• For natural science, relevant publications are listed on e.g.

PubMedCentral, where currently 1551 journals are indexed. • In 2006 there were 1.35 Mio peer-reviewed single publications.

How to save time? How to find the right one?

How to find all relevant ones?

NIC Public Access, February 08, 2013 Scientometrics. 2010 September; 84(3): 575–603.

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How to find the good ones?

Literature databases There are many different databases with specific focus on scientific areas, however the most important ones for natural science are: PubMed Central (PMC) www.ncbi.nlm.nih.gov/pubmed Isi Web of Science www.isiknowledge.com/WOS BioMed Central www.biomedcentral.com Scopus http://www.scopus.com/home.url Google Scholar www.scholar.google.com scientific literature At ETH Zurich http://www.library.ethz.ch/ library of ETH Zurich, literature in general Basic setup of an efficient literature search is the same over all databases! The more specific the search query is, the fewer and better the results are

Providing two authors with initials gives more accurate hits than a subset of

the title or single words 14

peer-reviewed

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PubMed

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Refining a Search on PubMed

1. 2. 3. 4.

6.

8.

7.

5.

Exemplary PubMed Search:

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Exemplary PubMed Search:

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Exemplary PubMed Search:

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Exemplary PubMed Search:

AND OR NOT

Title Author Abstract PubDate Journal etc…

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Exemplary PubMed Search:

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Exemplary PubMed Search:

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Exemplary PubMed Search:

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Exemplary Google Scholar Search:

More indexed publications and journals than any other source! However usually not necessary.

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Exemplary Web of Science Search:

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Exemplary Web of Science Search:

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Exemplary Web of Science Search:

search queries similar to PubMed

Scopus

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How to retrieve the pdf’s: • Within the ETH network, one gets direct free access to the pdf’s of all journal which

ETH is paying for: Links from PubMed, Google Scholar or ISI WOS lead directly to pdf downloadable from the respective journals web pages • Open Access: Biomed Central (i.e. all the BMC journals are openAccess) • Author Manuscript typically also via BMC:

Authors are allowed to publish manuscript in advance upon acceptance (depending on journal) 29

ETH library Not all journals are linked from e.g. PubMed or ISI WOS http://www.library.ethz.ch/ E-Journals – Liste

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Reference Management, Alerts and Copyright

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Stay up-to-date

New results from academic research

• Groupmeeting

• Guest lectures

• Journal club

• New papers (automatic alert)

• Conferences

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Alerts

Different services allow email alerts

• Periodically per email

• Efficient way to find new papers

• Limited by the search query

• Pubmed Alert

• Google Scholar

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Pubmed Alert

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Pubmed Alert

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Google Scholar Alert

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Google Scholar Alert

example@example.com

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Google Scholar Alert

example@example.com

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Web of Science Citation Alert

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Web of Science Citation Alert

example@example.com

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Reference Management

Why?

• Keep the overview, organize pdfs

• Consistency with many citations

• Reference easy to introduce

• Management of not (yet) cited papers

• Programs: CiteULike, Mendeley ,Endnote, Jabref (LaTeX), Bibtex (LaTeX)

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Jabref

• Open Source, free, java-based

• Platform independent (Windows, Mac, Linux)

• LaTeX, OpenOffice and MS Word (Bibtex4Word)

• Can work with SQL database

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Jabref

LaTeX + BibTex LaTeX can be written in any text editor, preferable is an integration with BibTex however. Here are some popular choices: • Vim with plugin (vim latex, LaTeX-Box etc) • Emacs with AUCTeX and WhizzyTeX • Lyx (WYSIWG editor, like Word/LibreOffice/OpenOffice, very easy for beginners) • TeXnicCenter (Windows only) • Kile (Linux/KDE only) • Gummi (Linux only) • TeXShop (Mac only) • TeXworks • Texmaker

References: http://tex.stackexchange.com/questions/339/latex-editors-ides http://en.wikipedia.org/wiki/Comparison_of_TeX_editors

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Endnote

• Commercially, available for free through IDES at ETH

• Only Windows and Mac

• LaTeX, OpenOffice and MS Word

• Online search and download of papers

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Endnote

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CiteULike

• Webservice of Springer

• No dependency of local workstation

• Social bookmarking (“share references”)

• Export as Text, PDF or Bibtex file

• Import in Endnote / Jabref or directly in LaTeX

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CiteULike

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Mendeley • Web-based import via bookmark

• Synchronize with local Mendeley desktop installation

• Insert references into word, openoffice and latex

• Read and edit pdf within Mendeley

• Drag and drop addition of pdf via watched folders

• Social bookmarking via online profile

• So far free-ware

Due to file-sharing not allowed at ETH….

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Mendeley Web Import Bookmark

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Mendeley Web Interface

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Example: Word + Endnote

Word with EndNote Addin

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Initial EndNote window, create a library

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Empty library window of EndNote

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Setup online search database: PubMed

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Search yielding 909 hits, with one author.

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Search yielding 3 hits with two authors

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Within EndNote add in, select Style and insert citation

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Copyright

Under copyright are

“geistige Schöpfungen der Literatur und Kunst, die individuellen Charakter haben.” [Urheberrecht Art 2 CH]

• Citations are excluded from copyright

• Allowed is: own use, teaching

• Courts can decide over violations

• Rights belong to the publisher

• OpenAccess: Creative-Commons Licenses

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Academic ethos Goes beyond copyright

• Also ideas need to be referenced

• Correct citations are enforced (means that it enables one to find the

corresponding paper)

• Violations can be persecuted from the academic community (e.g. deprive

doctoral title)

• Example citation: Sherman J, McKay MJ, Ashman K, Molloy MP. MCP. vol. 8,

pp. 2051-2062, 2009

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ETH Guidelines http://www.ethz.ch/faculty/exams/plagiarism/index_EN It qualifies as plagiarism if an author:

• Uses another author’s work without citing the source

• Paraphrases another author’s work without citing the source

• Translates another author’s work without citing the source

• Submits the work of a ghost writer

• Submits the work of another author in his/her own name

• Cites the original author, but somewhere other than in the context of the extract

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How to do it right

• Cite all of your sources fully and verifiably, such that anyone can check them

• Differentiate clearly between your own work and that of others

• Place borrowed text (both sentences and concepts) in inverted commas

• If you have rendered text in your own words or summarized it, give its source in parentheses

• Identify a citation as a secondary source

• At the end of your paper list alphabetically all of the sources

• General knowledge does not require citation

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Practical Questions

• Copy a whole passage of text: Needs correct citations and only if the text so that significant

• Copy single ideas: Needs correct citations and discussion in that context

• Copy of a picture: Only with permission of the publisher (author alone is NOT enough, see Copyright) and correct citations. For OpenAccess publishers, different conditions apply.

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Final Exercises: • 4-5 groups (2 persons per group) will work on each exercise. Please ask for

control of each intermediate step if you are not sure.

• It is expected that you hand in a scientific report. This means that the report should only cite peer-reviewed scientific literature and not e.g. Wikipedia.

• Copy paste or write solutions into a word file, collect the references in a library file and reference them with word using the Endnote plugin.

• Final sign-out will be done individually for each group upon control.

• Send your word file (.doc) & library file (.enl) to fuhrer@imsb.biol.ethz.ch

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Final Exercises: There are 6 different exercises:

• Crabtree/Warburg Effect (about cancer metabolism)

• HIV therapy and drug resistance

• DNA encoded chemical libraries

• E. coli metabolism and enzyme kinetics

• FRET sensors (about reporter proteins)

• Streptococcus and infections thereby

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