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:

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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

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