Master space 2017

Master SPaCE -
Research information and
reference management
September 2017
caroline.peron@univ-amu.fr
1

1 / Information seeking strategies
2/ Improving my reference management with Zotero
Lesson plan
2

TITRE DE LA PRÉSENTATION
> TITRE DE LA PARTIE
1/ Information seeking
strategies
3

Some assignments will require you to locate your own sources relevant to a
specific research topic.
In natural sciences where information accrues rapidly and must be disseminated
quickly, journal articles are actually the researcher’s preferred means of
communication.
Scientists count as primary sources empirical articles published in peer-reviewed
journals. These published results of experiments and analyses of data provide
the raw material for other scientists to consider as they pursue their own
research.
Secondary sources in the sciences include literature reviews and books.
As you consult sources, you should always be asking yourself questions about
what a source adds to your understanding of a topic and how it might be helpful
to you as you write your own paper.
What types of information do I need in science ?
4

• Keyword searching is how you typically search web search engines.
• Subject headings describe the content of each item in a database. Use these headings
to find relevant items on the same topic. Searching by subject headings is the most
precise way to search article databases.
How to find subject headings ?
• Look to see if the database has an online thesaurus to browse for subjects that match
your topic.
• Start with a keyword search;
Browse the results;
Choose 2 or 3 that are relevant;
Look at the Subject or Descriptor field and note the terms used
Redo your search using those terms : your results will be more precise than your initial
keyword search.
Ex. Search on universe expansion on the Web of Science database
Keywords and subject headings
5

Termsciences is a terminology portal developed by INIST (National Institute
of Technical and Scientific Information).
Keywords and subject headings
6

They connect your seach words together to either narrow or broaden your set of results.
Use AND in a search to narrow your results and tell the database that ALL search terms must
be present in the resulting records
Ex : expansion and universe
Use OR in a search to connect two or more similar concepts (synonyms) and broaden your
results, telling the database that ANY of your search terms can be present in the resulting
records.
Ex : cosmology or astronomy
Use NOT in a search to exclude words from your search and narrow your search, telling the
database to ignore concepts that may be implied by your search terms.
Ex : universe not expansion
Boolean operators
7
/////
expansion
///////
///
////// ////
universe

• Truncation, also called stemming, is a technique
that broadens your search to include various word endings
and spellings.
Ex. Phys* = physical, physics, physicist
• Wildcards substitute a symbol for one letter of a word. This
is useful if a word is spelled in different ways, but still has
the same meaning.
Ex. colo?r = color, colour
Truncation and wildcards
8

• Most databases allow you to specify that adjacent words be searched as
phrases. Using parentheses or quotes around search words is a common way
to do phrase searching, but not all databases or search engines use them.
Ex. “gravitational lenses”
• Proximity operators : many databases allow you to specify that the words you
are searching are within a certain proximity of each other.
NEAR/# specifies that the words may appear in any order. Substitute the # with a
number of words that may appear in between.
Ex. Expansion NEAR/3 universe retrieves : expansion of universe, universe in
expansion etc…
Phrase searching tips
9

Locating resources
10
1010
I want to… I will find it in…
- Define a notion,
- Find a synthesis of avalaible
knowledge
- Dictionaries,
- Encyclopedias
(Universalis, Techniques
de l’Ingénieur)
- Deepen a problematic,
- Check assumptions
- Books,
- Scientific journals,
- Theses,
- Conference proceedings,
- Patents …

The Library Portal is the main entry point for information about the
university library system :
Environnement numérique de travail > BU >Site web BU
AMU library portal
11

AMU library portal
Tutorials and
disciplinary guides
Books, articles and
journals (printed or
online)
Library catalogue
Online question and
answer service
12

A catalogue is an organized, searchable listing of the library's
collection. There are 72 libraries at Aix-Marseille University : they
have 1 catalogue, listing their 1.4 million documents.
AMU library catalogue
13

Result list : refine your search by authors, libraries, topics…
14

Result details : location in the library, on the bookshelves; status (available/on
loan); other good terms to use (tags = sujets)…
15

Be careful : in the library catalogue, you will find journals, but you
have to check the online access of the articles! Articles are indexed in
databases or publisher website, such as Web of science, ScienceDirect,
IOP, APS…
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Reader account
17
You can log to your reader account with your university certificate and use
different services : loan renewals, purchase suggestions, place holds (a « book
shuttle » runs everyday between the four science libraries, St-Charles, Luminy,
Saint-Jérôme and Montperrin).

The « Système Universitaire de Documentation » (Sudoc) catalogue is
a French collective catalogue created by Higher Educational and
Research libraries and resource centres. There are nearly 10 million
bibliographic records in this catalogue describing all kinds of document
www.sudoc.abes.fr/
Once you have found an interesting document, you can ask for its loan
(each university library has an interlibrary-loan service).
Sudoc catalogue
18

University identifiers are required to access to many of the online
resources (subscription databases for example). Click on the tab
« Documentation ».
Our web site will change this fall
AMU library online resources
19

• Access by resource name or field :
http://bu.univ-amu.libguides.com/physique
20

• « Documents en ligne »
- research through library’s subscriptions and free resources using a single-
search box.
- access to 20 000 online journals (subscription or open access). Research by
journal title or field.
21

• Bibliographic databases
It is a database of bibliographic records, an organized digital collection of
references to published literature, including journal articles, conference
proceedings or books, published by different publishers.
They generally contain very rich subject descriptions in the form of
keywords, subject classification terms, or abstracts.
Ex: Web of Science
• Online journals
On the same website, a publisher gathers online articles, online
conference proceedings etc… The publisher may be specialized in one
field (IOP or APS for physics) or multidisciplinary (ex. Science Direct,
Springer, Wiley)
You may access to the article full text if the library has a subscription.
Not to be confused…
22

23
Our subscription to the Web of science includes Medline + Current
Contents Connect + Web of Science Core collection + Korean Journal
database +SciELO citation index
- Web of Science Core Collection, is a bibliographic database covering
more than 12 000 journals in sciences, social sciences, arts and
humanities since 1975.
It also includes :
- Conference Proceedings Citation Index (150 000 conference
proceedings since 2000).
- Index Chemicus, chemical database (since 1993)
- Update : weekly
Additional resources: Journal Citation Reports and Researcher ID
Online tutorial : https://www.youtube.com/user/WoSTraining
Selection criteria : http://wokinfo.com/media/essay/journal_selection_essay-en.pdf
Web of Science

24
• Basic search
Web of Science
Select AND, OR,
NOT
Search settings
: index,
timespan
Select search criteria :
topic, author,
publication name,
funding agency…

25
• Truncation and wildcards
* = Zero or more letters
Ex : phys* (physics, physical)
Ex : *oxide (peroxide, sulfoxide,
zinc oxide)
$ = Zero or one letter
Ex : lap$roscopic (laproscopic,
laparoscopic)
? = One letter
Ex : en?oblast (entoblast,
endoblast)
Web of Science
• Proximity operators
exact phrase (« »)
Ex : « stem cell »
SAME = use SAME to restrict your
search to terms that appear in the
same address within a Full Record
Ex : forest SAME fire, dans le
champ « topic »
NEAR/x = Use NEAR/x to find records
where the terms joined by the
operator are within a specified number
of words of each other.
Ex : Salmon NEAR virus = Salmon
NEAR/15 virus

26
• Result list : sort by publication date is set by default.
Search alert (only available using Web of Science Core Collection),
save and export results (print, mail, marked list, export to reference
management software).
Web of Science
Full text access if
the library has
subscribed to the
journal
Viewi citations and their
network in a timespan

27
• Result list:
Refine results using :
- keywords
- WOS categories,
- Document type,
- Research areas (wider than WOS categories),
- Funding agencies
- open access journals…
Web of Science

28
• Result details :
View Journal Information : données du Journal Citation Reports,
ISSN…
Related Records, liste des références en lien avec cet article ;
Citation Map : cartographie du réseau de citations de l’article
Texte intégral : full text (if the library has a subscription)
Web of Science

Journal Citation Reports : journal ranking by Impact Factor.
Number of citations 2013 +Number of citations 2012
Number of articles 2013 + Number of articles 2012
Web of Science
29
Ex. Impact Factor of a journal in 2014=

ScienceDirect : 2500 journal and 30000 ebooks of the
multidisciplinary publisher Elservier. The archives of more than
2200 journals published by Elsevier from 1823 to 2001, are
available thanks to the ISTEX project.
The library has not subscribed to the whole catalogue : the
12 million articles of SD are not all full text.
Daily updates.
Online tutorial :
http://help.sciencedirect.com/Content/tutorials/sd_menu.html
Science Direct
30

Springer Link is Springer’s online delivery platform, providing access
to 8 million documents of STM resources (2700 journals since 1997).
Springer
32

Wiley Online Library features 1500 journals, over 16,000 online books,
and hundreds of multi-volume reference works, databases, and other
resources (the library has not subscribed to the whole catalogue).
Thanks to the ISTEX project, we have access to the archives of 2 200
scientific journals from 1791 to 2011.
Wiley Online library
33

APS journals features 12 journals, especially Physical Review D which publishes
leading research in elementary particle physics, field theory, gravitation, and
cosmology. The archives of these journals are available on the database PROLA.
APS journals – American Physical Society
34

The library has access to 108 scientific journals published by IOP from
1874 to 2012 (ISTEX project).
IOP – Institute of Physics
35

« Open-access (OA) literature is digital, online, free of charge, and free of most
copyright and licensing restrictions”. (Peter Suber)
Most OA journals function on a peer review model that is every bit as stringent as
that of their traditional print counterparts. The "open" refers to the free availability
of research to the public, not to the removal of the refereeing process that has
been the basis of scholarly publishing for three centuries.
Open access literature includes both peer-reviewed journal articles and author
self-archived pre- and post-prints deposited in digital repositories.
• DOAJ : Directory of open access journals
• Open access repositories : OpenDOAR (directory of open access repositories)
; arXiv (the oldest repository) ; HAL (French repository); HAL-AMU (Aix-
Marseille University repository)…
Open access
36

A search engine is a service that uses a computer program
to search the Internet and identify items that match the
characters and keywords entered by a user.
Why use a search engine ?
Search engines are useful for finding information on
organizations, groups, and personal web pages related to a
topic. They can also be used for finding articles, but it can be
difficult to narrow down results, find relevant material, and
assess the legitimacy of information found on the Internet.
Search engines
37

Google Scholar is an online, freely accessible search engine that lets users look for
both physical and digital copies of articles. It searches a wide variety of sources, including
academic publishers, universities, and preprint depositories looking for: peer-reviewed
articles, theses, books, technical reports, abstracts, patents, reprints.
- GS is easy to search if you are familiar with the Google search engine
- it provides some basic and advanced search options,
- you can search a specific article title in Google Scholar to see how many times it has been
cited
- it provides direct access to full text of articles if they are available for free online
- it can link to library catalogs (including the University of Illinois catalog), helping you find
resources within your own library and beyond
- it does not contain an easy way to sort articles in your results list
- it does not clearly specify what type of material (academic journal, magazine, newspaper etc.)
is in the results list
- it provides full text of some electronic articles but is not as helpful in tracking down print
articles
Google Scholar
38
38

• Advanced search
Click on the arrow to the right of the search box. It'll bring up the advanced
search window that lets you search in the author, title, and publication fields, as
well as limit your search results by date.
filetype: ex : filetype:pdf « gravitational lenses »
author: author:falco « gravitational lenses"
intitle: put the paper's title in quotations
Google Scholar
39

GS can be linked with the library subscriptions.
Google Scholar
40

A web directory is an organized, categorized listings of Web sites,
put together by human reviewers. On the contrary, search engine
listings are put together by automated systems and lack a
navigable structure.
Directories place an emphasis on linking to site home pages and
try to minimize deep linking. This makes directories more useful
for finding sites instead of individual pages.
Web directory
41
41

Digital Library portal for researchers in Astronomy and Physics : more
than 12.2 million records in Astronomy, Astrophysics, Physics.
http://www.adsabs.harvard.edu/
https://ui.adsabs.harvard.edu/
ADS
42

Using research centres websites, or public institution websites can be useful .
Ex. HEASARC : The High-Energy Astrophysics Learning Center
http://heasarc.gsfc.nasa.gov/
Institutional websites

A serious game or applied game is a game designed for education and
training.
http://bu.univ-amu.libguides.com/seriousgames/seriousgames-sciences
https://phet.colorado.edu/fr/simulations/category/by-level/university
https://itunes.apple.com/fr/app/astronauts-zerog-free/id548674324?mt=8
Let’s play/learn with serious games !
44

TITRE DE LA PRÉSENTATION
> TITRE DE LA PARTIE
Improving my reference
management with Zotero
45

Essential for scholarly reading and writing.
All your bibliographic references are gathered in one database.
A reference manager software can :
- import references from online bibliographic databases (Web of
science, PubMed…)
- share references between different computers and/or users
- store scholarly references on your computer
- create a bibliography on a word processor
What is a reference manager software ?
46

Many choices :
Selection criteria :
- Cost : free to use or personal/institutional license ?
- User interface : easy to learn/ to use ?
- Web storage space : online backup of your references
- Reference management (organization of references, citation plugin for
Word/Open office…)
- Metadata extraction technology (extraction of DOIs, embedded metadata
from PDFs)
- Collaboration (private/public groups, social network)
- Technical support (user forum)
How to choose my reference manager software ?
47

How to choose my reference manager software ?
48
M. Fenner, K. Scheliga, Reference
Management, Opening science,
http://book.openingscience.org/tools/
reference_management.html ;
http://www.hiig.de/en/reference-
management/

• Free and open source (Firefox plugin), easy to use.
• Automatic capture of citation information from web pages.
• Wide variety of import/export options.
• Formated citation export (style list).
• Integration with Microsoft Word and Libre Office.
• Storage of PDFs, links, web pages.
• Advanced search tools (fast search through your references).
• Financed by well known institution (Roy Rosenzweig Center for
History and New Media > George Mason University)
Interesting features of Zotero
49

Use an updated version of Firefox.
The latest version of Zotero : 4.0 (February, 2015).
Allow the software installation by clicking on « Install now »
http://www.zotero.org/download/
Successfully installed :
Install Zotero
50

Zotero Standalone runs as a separate application and plugs into your
browser (Google Chrome, Safari).
Zotero Standalone
51

Zotero interface
52
Toolbar
Files and
tags list
References
Details on the
selected
reference

First step
How to integrate and organize your references
53

• Add citations to Zotero library :
New citation, added manually
From a Web page
From its identifier (ISBN, DOI, PMID)
From a compatible site or database (Google Scholar, Web of Science)
- Add attachments to a reference
- Import reference files
Toolbar
54

Compatible sites list : http://www.zotero.org/translators/
A folder icon will appear next the Zotero icon. Click on it.
Example : Google Scholar
Importing citations from compatible databases and sites
55

Ex: Web of Science, Science Direct, ACS, RSC, Wiley, PubMed,Optics
Infobase, Google Scholar, Sudoc…
Importing citations from compatible databases and sites
56

Export your citations and save them as a RIS or BibTeX file on your
Desk. Then import this file with the gear icon
Ex: Reaxys, Scifinder
Importing citations from non compatible databases
57

Creating citations manually
58

Click on the « save the current webpage in Zotero » icon
Saving webpages
59

Click on this Identifier icon to create citation from an
identifier : ISBN, DOI, or PubMed ID.
Creating citations from an identifier
60

Drag your PDF into your Zotero library :
Importing reference by retrieving PDF metadata
61

Right click on the selected PDF, « Retrieve metadata for the PDF’s » and install
a plugin the first time :
If Zotero can find the PDF in Google Scholar, it creates a new library item for the
paper, downloads the citation information and attaches the original PDF to the
new item.
Importing reference by retrieving PDF metadata
62

To enter notes, click on New Note icon :
To create a note from a reference : click on « Add Child Note »
You can attach files to individual citations in your library, using the New Child
Attachments icon :
Creating notes and attachments
63

Highlight the text that you would like to cite
Right-click on the text and click on « create Zotero Item and Note from
Selection »
Creating note from a web page
64

Zotero doesn’t propose that feature.
You have to use another PDF reader than Acrobat :
- PDF X-Change Viewer for Windows (http://pdf-xchange-viewer.softonic.fr/)
or Nitro PDF reader (http://www.nitroreader.com/fr/)
- Skim for Mac (http://skim-app.sourceforge.net/)
Adding note and highlighting PDFs
65

In the toolbar, you can choose how to classify your references.
Organize your Zotero library
66

« My library »
Create a new collection/folder
Drag and drop the collections to create a file tree :
Zotero detects duplicates :
Organize your Zotero library
67

Quick searching
Advanced searching :
Search for citations in your Zotero library
68

Click on a tag to see items with that specific tag
Search for citations with tags
69
Search by
selected tag
Tags of the selected
reference (created by
you or downloaded
automatically with
records from
databases)

Zotero 4.0 lets you assign to up to 6 of your favourite
tags to highlight important “to read” articles that you
would like to find quickly at a glance.
Search for citations with tags
70

Create a link between one item and another by clinking on
the « Related » tab :
Add relationships
71
2 related references

Right click on the selected item. Choose « Delete selected item from
library ».
This deleted item will be stored in the « Waste basket »
Delete citations
72

Second step
How to create a bibliography and share your references
73

You can insert a citation very easily by dragging and
droping your citation :
Citation style can be set up by clicking on the « Actions »
icon .
Cite while you write
74

•Plug-in Word/Open Office :
http://www.zotero.org/support/word_processor_plugin_installation
( Zotero icons are available in the « Adds-in » or « Zotero » tab in Word)
Using Zotero with Word
75

Insert a bibliography
Edit a citation (You have to place the cursor inside the relevant
citation before pressing this icon )
Edit a bibliography
Refresh : If you have made changes to your collection, once you
inserted a citation or created a
bibliography, click Zotero Refresh. This will update your references in
your document.
Change the citation style
http://www.zotero.org/support/word_processor_plugin_usage
76

The 1st time you insert a citation (using the icon ) , you will have to
choose a citation style.
Choose citation styles in « Zotero Style repository » (8813 styles - September
2017): http://www.zotero.org/styles
77

•Setting up your Cite preferences
The default option when making a selection to cite a reference :
"Classic View" is not the default option when you download Zotero, but it is a
useful option to set up as your preferences:
-Click on the Actions (gear) menu.
-Select Preferences on your drop down menu.
-Select "Cite" in your Preferences box.
-Check the "Classic Add Citation Dialog" option.
78

Imports/export on BibTeX :
- Right-click on the selected reference.
- Zotero generates types, fields…
Using Zotero with LaTeX
MIT and EPFL guides to create bibliographies using
Zotero and LaTeX

Zotero Better Bib(La)TeX enables to :
-Set your own citation keys
-Drag and drop citations in a LaTeX editor
-Have configurable citekey generator and cleaner (de)LaTeXifier
https://www.zotero.org/support/plugins
https://zotplus.github.io/better-bibtex/Citation-Keys.html
Using Zotero with LaTeX

• Zotero's online syncing allows you to access your Zotero library on any
computer with internet access. Each Zotero user is given 300 MB of free Zotero
File Storage for attached files.
• 1st step to syncing your Zotero library : create a Zotero account
Then open Zotero's Sync preferences tab and enter your login information in
the Zotero Sync Server section :
Zotero’s online syncing
81

Your library online :
You can sync manually at any time by clicking the “Sync with Zotero Server”
button.
Zotero’s online syncing
82
http://research.library.gsu.edu/content.php?pid=24410&sid=332122

With the release of Zotero version 4.0, it is now possible to choose which
directory Zotero uses when you attach links to files. If you use Dropbox Basic
(2Go of free storage), you can now save your citations in Zotero, attach links to
files in a Dropbox folder, and have both synchronize with every computer you
use.
http://libguides.princeton.edu/content.php?pid=31604&sid=3799749
Syncing with Dropbox
83

Zotero allows you to export your Zotero library as a Zotero RDF file to
copy your library.
Export your Zotero library
84

Zotero groups, enables you to collaborate with project
members, and set up web-based bibliographies for classes
you teach.
Share your own work or sources you have discovered
with others who are working in related areas.
Collaborate with colleagues, publicly or privately, on
ongoing research.
Discover other people with similar interests and the
sources they are citing.
Zotero groups
85

Private Groups
Only group members and users invited to join the group are able to
see the group’s page.
Private groups are completely hidden from group searches. They are
not shown on members’ public profile pages and will not appear in search
engine results.
Public, Closed Membership
Anyone can view the group page, but the only way to join the group
is by invitation or by requesting an invitation.
If the group has a public library, administrators can choose to show or
hide the entire library or individual collections from non-members.
Public, Open Membership
The group page is public, and anyone who wants to can join instantly.
If the group has a public library, administrators can choose to show or
hide the entire library or individual collections from non-members.
Zotero groups
87

• Select “Output Styles” from the Edit menu.
From the list of output styles select RefMan (RIS).
• Select “Export” from the File menu.
In the Export window that pops up, choose “Text Only”, select the RIS output style
immediately below “Text Only” in the dialog, and hit “Save.”
• After exporting from EndNote, click on the gear icon in your Zotero pane and
select « Import » from the pull-down menu.
• In the file system window that pops up, locate the RIS file you exported from
EndNote and select “Open.” Your references should be imported into Zotero.
The same basic steps apply to many other reference management systems.
http://www.zotero.org/support/kb/importing_records_from_endnote
Export your EndNote library to Zotero
88

Export a bibliography from Word to Zotero
89
Use a parser like Wizfolio : http://wizfolio.com/

Zotero quick start guide : http://www.zotero.org/support/quick_start_guide
Beginner’s guide to using Zotero (University of British Columbia) :
http://www.slideshare.net/giustinid/beginners-guide-to-zotero
Backing up your Zotero library :
http://libguides.northwestern.edu/content.php?pid=68444&sid=676064
Requesting styles on Zotero forum : https://github.com/citation-style-
language/styles/wiki/Requesting-Styles
Editing style with CSL editor (collaboration between Columbia University
Libraries and Mendeley) :
http://editor.citationstyles.org/about/
Useful links
90

If you have a question about research information,
please contact me :
caroline.peron@univ-amu.fr
or contact our online Q&A service : http://univ-
amu.libanswers.com/
91

Master space 2017

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