Scientific Source Management - Thomas Kaiser, Institute of Applied Physics - Uni Jena
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Scientific Source Management Thomas Kaiser, Institute of Applied Physics
2
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.
3 Overview How Science works…
4
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
5
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!
http://en.wikipedia.org/wiki/Albert_Einstein#/media/File
:Einstein_1921_by_F_Schmutzer_-_restoration.jpg
(accessed on 09.6.2015)
6
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!
7 Scientific Literature
8
Scientific Literature
Types of Scientific Literature:
• Books
• Review Articles
• Full-length Papers
• Letter articles
• Proceedings
• Nature / Science articles („Big Bang“)
9
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!
10
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 field11
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 topic12
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 area13
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' journals14
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
• Science15 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
16 Scientific Databases Your primary source of information
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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 here18
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 → Scitation19
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)
• ...20
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)
• ...21
Publishers’ Databases
most common / important journal resources:
• Letter Articles:
• Phys. Rev. Lett. (APS)
• Opt. Letters (OSA)
• Appl. Phys. Lett. (AIP)
• ...22
Publishers’ Databases
most common / important journal resources:
• Proceedings:
• OSA Conferences
→ OpticsInfoBase
• SPIE Digital Library
(no direct access)
• IEEEexplore23 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
24
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 metrics25
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 Factor26 ISI Web of Science
27 ISI Web of Science
28 ISI Web of Science citation map
29 ISI Web of Science Impact Factor
30 ISI Web of Science H index
31
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.optics32
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???33
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
here34 Literature management How does it work? • publishers provide reference data for a paper • this is imported into BMS which does the rest
35
Literature management
Example: BibTeX & JabRef:
BibTeX
data
for this
paper JabRef
myrefs.bib BibTeX database
file36 Literature management Example: BibTeX & JabRef:
37
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}38
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)39
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. bibtex4word40
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!)41 Literature management
42 Literature management
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