Reference Management Course 2015: Complete Materials

Dasapta Erwin Irawan
Faculty of Earth Sciences and Technology
Institut Teknologi Bandung
19 January 2015
Reference management
A mini course 0
Image: flickr/jasonparis
COMPLETE MATERIALS

A bit about me
●
A bit old: born in 1976
●
A bit hard: hydrogeology
●
A bit old-skool: love vintage things
●
A bit old-fashioned: nodye and weird hair cut
● A bit social:
– On Facebook: https://www.facebook.com/dasaptaerwin
– On Twitter: @dasaptaerwin
– On ResearchGate: www.researchgate.net/dasapta_irawan

Disclaimer
● This mini course is non-credit.
● It is offered as opportunities for students to learn
specific skills in just a few sessions.
● This mini course offers no warranty of your study
performance.
● Consultation session with your supervisor is very
important to make the best out of this mini course.
● I'm prone to error, please report any typos or
misconceptions from reading this doc.

Part 1: intro to reference management
● 1.1 common problems and solutions
– the common problems in scientific writing
(papers, thesis, dissertation)
– the common mistakes in writing
– the tools and proposed solutions

● 1.2 What is reference management
– How does it help to our writing and what are the
tools needed
– Where to get the softwares and why does it have
to be opensource
– How to install Reference Manager and connect it
to our word processor

Part 2: how to retrieve references
● 2.1 Where to find:
– Library and its website
– Databases:
● Free: Google Scholar[13] (free),
● ITB subscription: Scopus[10], Web of science[15],
ITB Library (http://www.lib.itb.ac.id/e-journal, )
http://www.lib.itb.ac.id/e-book

● Publishers:
– Conventional: Sciencedirect[17] (options:
conventional, open access), Elsevier[18] (options:
conventional, open access), Springer Sciences[19]
(options: conventional, open access)
– Open access: DOAJ[20], PeerJ[21], HESS[22],
PLOSone[23], ArXiv[24]etc

● Community, social media:
– ResearchGate,
– Academia,
– ResearchID.

● 2.2 tweaking the keywords
– What is a keyword
– What is keyword's operator
– How to get the best search results
– Use "Google Scholar" alert notification
– How to store the information

Part 3: how to store your references
● 3.1 how to store your references
– Saving the pdfs and metadata
– Folder structure

Part 3: how to store your references
● 3.2 how to use reference manager
– Importing, Organizing, and Taking notes
– Using and adding Citation style
– Citing and Making bibliography

Part 4: how to cite
● 4.1 Citation style
● 4.2 Paraphrasing
● 4.3 Plagiarism
● 4.4 how to use "Cite While You Write"

References
[1] Creative Common License site, https://creativecommons.org/licenses/, accessed 15 November 2014.
[2] Zotero site, http://www.zotero.org, accessed 15 November 2014.
[3] Mendeley site, http://www.mendeley.org, accessed 15 November 2014.
[4] Docear site, http://www.docear.org, accessed 15 November 2014.
[5] Endnote (Thomson Reuters) site, http://www.endnote.com, accessed 15 November 2014.
[6] Evernote site, http://www.evernote.com, accessed 15 November 2014.
[7] Growly Note site, http://www.growlybird.com, accessed 15 November 2014.
[8] Microsoft OneNote site, http://www.onenote.com , accessed 15 November 2014.
[9] MaxPlanck Institute of Biochem site,https://www.biochem.mpg.de/en/facilities/ivs/BibMgmt, accessed 15 November 2014.
[10] Scopus scientific database site, http://www.scopus.com, accessed 15 November 2014.
[11] Wikipedia Free Encyclopedia site, http://en.wikipedia.org, accessed 15 November 2014.
[12] JabRef site, http://jabref.sourceforge.net/, accessed 15 November 2014.
[13] BibDesk site, http://bibdesk.sourceforge.net/, accessed 15 November 2014.
[14] Google Scholar site, http://scholar.google.com, accessed 15 November 2014.
[15] Web of Science/Knowledge site, http://thomsonreuters.com/thomson-reuters-web-of-science/, accessed 15 November 2014
[16] ITB Library site, http://www.lib.itb.ac.id, accessed 15 November 2014.
[17] ScienceDirect Database site, http://www.sciencedirect.com, accessed 15 November 2014.
[18] Elsevier Site, http://www.elsevier.com, accessed 15 November 2014.
[19] Springer Sciences site, http://www.springer.com, accessed 15 November 2014.
[20] DOAJ, http://www.doaj.org, accessed 15 November 2014.
[21] PeerJ, http://www.peerj.com, accessed 15 November 2014.
[22] HESS, http://www.hydrol-earth-syst-sci.net/, accessed 15 November 2014.
[23] PLOS one site, http://www.plosone.org/, accessed 15 November 2014.
[24] ArXiv site, http://www.arxiv.org, accessed 15 November 2014.

19 January 2015
A mini course_1_1

DEI, ITB 3
What is reference/citation
management systems[9]
A system used for
{Storing}
{Organizing}
and
{Sharing}
reference collections

5
– common problems in scientific writing (papers,
thesis, dissertation)
– common mistakes in writing
– the proposed tools and solutions

6
– How does it {help} to our writing and what are the
tools needed
– Where to get the {apps} and why does it have to
be opensource
– How to {install} Reference Manager and connect it
to our word processor

7
common problems in scientific writing
●
Don't know where to {start}.

8
●
Don't know {where}to look for
informations.

9
●
Don't know {how}to look for
informations.

10
common problems in scientific writing (papers,
● Don't know how to give credits
{cite} for informations.

11
common mistakes in writing
● {Non-flowing} structure and/or story

12
● {Misplaced} component

13
● {Bad} referencing/citing

14
the tools and proposed solutions
● Start from the end
{Bibliography}

15
● Use a
{reference management system}

16
● Keep a {log book} or binder

17
●
Keep a {digital} log book or
binder

18
●
Use the appropriate {apps}
– Zotero[2], Mendeley[3], Docear[4],
JabRef[12], BibDesk[13], etc
– EndNote[5]

19
●
Use the appropriate {apps}
– Evernote[6],
– GrowlyNote[7],
– Ms OneNote[8]

20
References

19 January 2015
A mini course_1_2

4
– common problems in scientific writing (papers,
– common mistakes in writing
– the proposed tools and solutions

5
– How does it {help} to our writing and what are
the tools needed
– Where to get the {apps} and why does it have
to be opensource
– How to {install} Reference Manager and
connect it to our word processor

DEI, ITB 6
What is reference/citation
management systems[9]
A system used for
{Storing}
{Organizing}
and
{Sharing}
reference collections

7
How does it {help}
● {Get} ideas

8
How does it {help}
● {Choose} ideas

9
How does it {help}
● {Formulate} ideas

10
How does it {help}
● {Keep track} of your ideas

11
How does it {help}
●
Build one of multiple {digital}
library(ies) and reading list(s)

12
How does it {help}
●
Organize your {pdfs}

13
How does it {help}
●
Based on {topics/ideas}

14
what are the tools needed
● {Apps:} Reference/citation manager
●
We will use {Zotero}[2]
● Read also: Wikipedia[11]

15
what are the tools needed
●
{database/index}: Reference/citation
manager
●
We will use {Scopus}[10]
● Read also: Wikipedia[11]

16
References

Dasapta Erwin Irawan 1
19 January 2015
A mini course 2_1_1

Outline

● 2.1 Where to find:
– Library and its website
– Databases:
● Free: Google Scholar[13] (free),
● ITB subscription: Scopus[10], Web of science[15],
ITB Library (http://www.lib.itb.ac.id/e-journal, )
http://www.lib.itb.ac.id/e-book

● Publishers:
– Conventional: Sciencedirect[17] (options:
conventional, open access), Elsevier[18] (options:
conventional, open access), Springer Sciences[19]
(options: conventional, open access)
– Open access: DOAJ[20], PeerJ[21], HESS[22],
PLOSone[23], ArXiv[24]etc

● Community, social media:
– ResearchGate,
– Academia,
– ResearchID.

● 2.2 tweaking the keywords
– What is a keyword
– What is keyword's operator
– How to get the best search results
– Use "Google Scholar" alert notification
– How to store the information

Where to {find}
{Conventional} library
flickr/mellydoll

Where to{find}
{Digital} library

Where to{find}
● Databases/indexes: Google Scholar[13]
Free, can be accessed anywhere,
cloud based
Provides research profile,
email notification
Mature platform
Massive results
Need more filtering
Limited analysis

Where to{find}
● Databases/indexes: Google Scholar[13]
● Email notification: for new citation or new papers

Where to{find}
● Email notification: for new citation

Where to{find}
● Email notification: new papers

Where to{find}
●
How to {get} it?
– Set up a Google
account
– Go to alert

Where to{find}
●
How to {get} it?
– Set up a Google
account
– Go to alert
– Create alert

Where to{find}
●
How to {get} it?
– Set up a Google
account
– Go to alert
– Create alert
– Enter your
keywords and
email

Tweaking your keywords
●
What is {keywords}?
– Keywords are the words that academics use to
{reveal the internal structure}of an
author's reasoning[11].

●
What is {keywords search}?
– Keyword research' is a practice used by search
engine optimization professionals to find and
research actual {search terms}people
enter into the search engines when conducting
a search[11].

● How to get keywords?
– {Read} and {listen} more

– Try {Google Trends} to get more
combinations (http://www.google.com/trends/

– Try {Google Trends} to get more combinations (http://www.google.com/trends/
– Use {operators}:
● (AND) ------------------------> hydrogeology (AND) regional planning
● (OR) ---------------------------> hydrogeology (OR) regional planning
● “key 1 key 2” ------------------> “hydrogeology regional planning”
● Allintitle: keywords –--------→ allintitle: hydrogeology regional planning
● Allintext: keywords –--------→ allintext: hydrogeology regional planning
● Author: “name” –-------------> author: Irawan, DE ; author: “Dasapta Erwin”
● Site: “site” ----------------------> “hydrogeology regional planning” site:flickr.com
● Filetype:“pdf, doc, xls, etc” → “hydrogeology regional planning” filetype:pdf

– Try {Google Trends} to get more combinations (
http://www.google.com/trends/
– Use {operators}:
– Use {multiple} sets of keywords
– Use {advanced search} mode

Let's try it out
● Use database:
– Google Scholar
– Scopus

Which one to choose?
● Strongly depends on your {purpose}?

● Use the following {criteria}:
– Number of docs found: use one with the {lowest}
results

● Use the following {criteria}:
– Number of docs found: use one with the {lowest} results
– Type of docs found: use one with the most {complete}
types:
● Peer-reviewed papers
● Conference proceedings
● Technical reports

Now let's try using Scopus
● In class practice

19 January 2015
A mini course_2_1_2

How to store the information?
● {Citation info} is very important.
●
What is {it}?
●
It's the {metadata} of a doc
●
Contains {important info} of the doc: title,
author, year, abstract, journal, etc

●
What is {BibTex} format?
– Is one of the widely used citation info format
– Text {ASCII} based, so it's {universal}
– You can use it with any citation manager apps:
Zotero, Mendeley, EndNote, etc
– {RIS} format is also text based

● Are there any other citation info formats?
– Yes, it's called {binary} format
– It can only be read by specific associated app
– Eg: {ENL} (EndNote), etc

●
How to get {citation info}?
– Look for button or menu
– {Cite} or
– {Export citation} or
– {Download citation}

{Copy and paste} these lines into a text file
Save as {*.bib}
Then import it using “new item” from {Zotero}

●
How to store {citation info}?
{Copy and paste} these lines into a text file
Save as {*.bib}
Then import it using “new item” from {Zotero}

How to store it?
Or,
There's other easier way
Use Zotero for Firefox add-on
Mendeley has it too
There's add-on for Chrome
But, AFAIK it doesn't work as smooth as in Firefox

Now let's try some exercise
Have you downloaded and installed Zotero's:
● standalone app?
● Firefox add-on
● LibreOffice/MsWord connector
● Go to Zotero.org

Now let's try some exercise
● Getting citation info from Google Scholar
● Getting citation info from Scopus
● Store it into Zotero Library

19 January 2015
A mini course_2_2

Let's try some inclass exercise
● Go to to any other databases
● Eg:
– ArXiv.org
– Sciencedirect.com
– Proquest.com
– Etc

● Use your own sets of keywords

● Do some analysis
● Eg:
– How many docs in the results
– What types of doc
– How is the yearly distribution
– What are the author's affilitions
– What are the author's country of origins

● Store the citation in your Zotero library
● Attach the associated pdfs

● Try to make some notes on a selected paper

19 January 2015
A mini course_3
Using Zotero

Outline
● 3.1 Terms in Zotero
● 3.2 Adding item
● 3.3 Attaching pdf
● 3.4 Adding notes
● 3.5 Choosing and adding citation style (csl)
● 3.6 Searching item
● 3.7 Exporting library, collection, sub collection
● 3.8 Syncing library
● 3.9 Connecting Zotero to Firefox
● 3.10 Connecting Zotero to word processor:
– 3.10.1 LibreOffice
– 3.10.2 Microsoft Word

Here we call a paper as an "item"
an item/a paper

A collection is group of papers, with the same topic
Screen Shot 2015-01-19 at
5.49.55 AM.png

A subcollection is a group of papers, with the same su
Screen Shot 2015-01-19 at
5.50.25 AM.png

A library is a complete list of your papers, collections,
a library

Automatic mode: Entering the DOI/ISBN

You can add some notes/ paraphrase here

Zotero's CSL library, search, and download

This is why you need to make an acc

How to connect to Firefox: store info directly from Fir

Zotero detects the available results, select

Zotero saving the docs, in the cloud

How to connect LO and MSW with Zotero

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