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TRANSCRIPT
Scientific Source Management
Thomas Kaiser, Institute of Applied Physics
Outline
Overview – how Science (really) works
• Good scientific practice
• Sources of Scientific Information
• Google, Wikipedia, … and what else?
Scientific Literature
Access to papers behind paywalls via FSU VPN
Scientific Databases – your primary source of information
• OPAC
• Web of Science ($$$)
• arXiv
Citation Management Software
• BibTeX
• Mendeley, EndNote etc.
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Overview
How Science works…
Overview
How Science really works…
• Science is a collaborative effort! Many people contribute over different
time scales.
• This requires that the individual scientist knows about the work of others
and exchanges ideas with them.
• This happens via:
• Conferences / Meetings / Workshops etc.
• Guest Professorships / Scientists in Residence / exchange programs
• Scientific Collaborations / Joint Projects etc.
• Scientific Literature
• Science requires proper acknowledgement of ideas citations
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Good Scientific Practice
• Everything (idea, formula, theory, image, …) that was not originally created
by you, needs the citation of the source!!!
(unless it is not obvious and commonly known, e.g. “Schrödinger equation”)
• This ensures a transparent “path of knowledge” in scientific results:
• reproducibility
• responsibility
• reliability
• Often required by copyright / intellectual property
regulations!
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http://en.wikipedia.org/wiki/Albert_Einstein#/media/File
:Einstein_1921_by_F_Schmutzer_-_restoration.jpg
(accessed on 09.6.2015)
Google, Wikipedia … and what else?
• Information? No problem! “Let me google that for you”: link
• Most people are not aware that Google is a highly unspecific and
personalized “source”!
• Wikipedia articles are flowing information (non-permanent!)
• Expertise of authors often not transparent
• Wikipedia is NO source for scientific information!
• Wikipedia can just be a “guide” TO scientific information IF the articles
are properly referenced themselves!
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Scientific Literature
Scientific Literature
Types of Scientific Literature:
• Books
• Review Articles
• Full-length Papers
• Letter articles
• Proceedings
• Nature / Science articles („Big Bang“)
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Scientific Literature
different types of publications:
reading the right thing
•Books:
• ideal to get a first overview over a new topic
• teach basic principles & techniques
• contain references to high-quality in-depth research
• not entirely state-of-the-art
• don't read everything!
Identify what you need for your work!
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Scientific Literature
different types of publications:
reading the right thing
•Review Articles:
• more specialized
• several 10 up to several 100 pages
• summarize the research of several groups
• cover a specific research area in detail
• still have the pedagogical aspect of books but are more up-
to-date
• written by high-reputation authors who are leading in the field
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Scientific Literature
different types of publications:
reading the right thing
•Full-Length Articles:
• most common form of scientific report
• often ~8-15 pages, also more
• in-depth treatment of a certain aspect
• information about details like e.g. experimental setup
• comprehensive presentation of new scientific contributions
• best to learn about specific aspects of your topic
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Scientific Literature
different types of publications:
reading the right thing
•Letter Articles:
• 'recent breakthroughs'
• 3-4 pages only
• latest developments in a field
• achievement of certain goals in a scientific topic
• no in-depth treatment or details
• best to learn about latest developments in a research area
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Scientific Literature
different types of publications:
reading the right thing
• Inproceedings:
• varying length
• summarize conference contributions
• only suitable if you attended the conference, otherwise often
difficult to understand
• content often also published in 'real' journals
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Scientific Literature
different types of publications:
reading the right thing
• 'Big Bang Articles'
• only breathtaking breakthroughs
• varying length
• are regarded as driving force for whole research
developments
• just highly polished articles
• Nature / Nature Physics / Nature Photonics → NPG
• Science
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Access to papers behind paywalls – FSU VPN
• Access to published papers needs to be payd if the journal is not open source
• ThULB has subscriptions to most important journals and provides it for you
• Normally, publisher
recognizes
subscriptions
via IP (141.35.x.x)
• VPN allows you
to access papers
from at home
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Scientific Databases
Your primary source of information
Scientific Databases
Where to find all these papers?
• Google (Scholar)
… ??? …
• Publishers Databases
• OPAC library catalogue
• ISI Web of Science
(They do it for money!)
• PubMed
• NASA ADS
…
see representative list here
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Publishers’ Databases
all publishers have their own online portal where you can get to the different
journals they publish → extensive search / Newsfeed functionality!
•APS → PROLA
•OSA → OSA Publishing
•Elsevier → ScienceDirect
•Wiley → Wiley Online Library
•IOP → IOPscience
•Springer → SpringerLink
•AIP → Scitation
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Publishers’ Databases
most common / important journal resources:
• Review articles:
•Reviews of Modern Physics (APS)
•Physics Reports (Elsevier)
•Reports on Progress in Physics (IOP)
•Advances in Optics & Photonics (OSA)
•Laser & Photonics Reviews (Wiley)
•...
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Publishers’ Databases
most common / important journal resources:
• Full-Length Articles:
•Phys. Rev. A / B / E (despite name!)
(APS)
•JOSA A / B, Optics Express (OSA)
•J. of Applied Physics (AIP)
•Applied Physics B (Springer)
•Optics Communications (Elsevier)
•...
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Publishers’ Databases
most common / important journal resources:
• Letter Articles:
•Phys. Rev. Lett. (APS)
•Opt. Letters (OSA)
•Appl. Phys. Lett. (AIP)
•...
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Publishers’ Databases
most common / important journal resources:
• Proceedings:
•OSA Conferences
→ OpticsInfoBase
•SPIE Digital Library
(no direct access)
•IEEEexplore
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OPAC library catalogue
books most important source of information for undergrads!
http://kataloge.thulb.uni-jena.de/DB=1/LNG=DU/SID=4fdcae39-0/LNG=EN/
all German libraries are connected
• system of getting you the publication you need
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Thomson Reuters Web of Science
• Non-free service, created by Eugene Garfield, the father of scientific
indexing, Link
• All the “official” data accumulates here
• Extensive information on
• WHAT papers exist on a topic
• WHO is publishing
• WHO is citing H index
• WHERE is the research published
• HOW MUCH is this recognized Journal Impact Factors
• WHEN does publication activity reach top timeline statistics
• WHERE do people (authors, citing) come from
• WHAT networks exist among them self citation metrics
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ISI Web of Science
What can it do for me?
• SEARCH
• comprehensive search capabilities (topical, time-resolved, geographic, …)
• scriptable as news feed / e-Mail alert
• IDENTIFY connections between different works
• for- / backward referencing
• geographical connections
• ALERT you when something new comes up
• PERSONALIZE science
• who is working in the field
• citation metrics (H index)
• MEASURE journal “performance”
• Impact Factor
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ISI Web of Science 26
ISI Web of Science 27
ISI Web of Science
citation map
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ISI Web of Science
Impact Factor
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ISI Web of Science
H index
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preprint servers - arXiv
important scientific role: preprint servers
• all types of articles available
• uploaded prior to peer-review
• freely accessible without subscription
• might only be feasible to experienced scientist due to 'everyone can
publish' philosophy → high number of papers might be confusing to
beginners!
• most famous: arXiv (Cornell Library), esp. category physics.optics
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Literature management
now you have
• gained an overview by looking into a basics textbook
• got deeper by crosschecking original references therein
• indentified people / research groups in the topic
stay up to date with e-alerts & custom news feeds
HOW TO KEEP TRACK OF
ALL THOSE PAPERS???
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Literature management
• use bibliographic management software!
What is it?
• BMS manages all your references in a database
• eases citation of a paper by integration into word processing software ('click
+ cite')
• provides tools for annotating, grouping, sorting & searching papers you
work with
most prominent: BibTeX (quasi-standard), EndNote, Mendeley, Qiqqa, see list
here
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Literature management
How does it work?
• publishers provide reference data for a paper
• this is imported into BMS which does the rest
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Literature management
Example: BibTeX & JabRef:
BibTeX data for this paper JabRef
BibTeX database file
myrefs.bib
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Literature management
Example: BibTeX & JabRef:
• LaTeX:
\documentclass{article} ... \begin{document} … bla bla bla … It was shown by \cite{Lalanne2000a} that Photonics is the most awesome thing in the world. … bla bla bla ... \bibliography{myrefs.bib} \bibliographystyle{authoryear} \end{document}
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Literature management
Example: BibTeX & JabRef:
• LaTeX:
… bla bla bla … It was shown by [1] that Photonics is the most awesome thing in the world. … bla bla bla ... References [1] P. Lalanne, & E. Silberstein, Fourier-Modal Methods applied to waveguide computational problems, Optics Letters 25, p. 1092, (2000)
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Literature management
Example: BibTeX – How to cite?
• MS Word / OpenOffice
• Plugins which can sync with a bib file and automatically create the
bibliography
• e.g. bibtex4word
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Literature management
Annoyed of importing the bibtex data by hand?
Looking for a 'one click' solution?
→ Try for instance Mendeley, Quiqqa, Papers etc.
• can import ref data directly from a website
• can scan a PDF automatically! (Drag & Drop)
• can synchronize among different PCs & web via client ↔ server
communication
• synchronizes with a bib file automatically if you wish
• brings MS Word & Open Office plugins for direct citation (very easy!)
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Literature management 41
Literature management 42