Reference Management Course 2015: Complete Materials

Dasapta Erwin Irawan

Faculty of Earth Sciences and TechnologyInstitut Teknologi Bandung

19 January 2015

Reference management A mini course 0

Image: flickr/jasonparis

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: no dye 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.

Available CC license[1]

License for this doc[1]

Outline

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

Reference management A mini course_1_1

DEI, ITB 3

What is reference/citation management systems[9]

A system used for {Storing} {Organizing}

{Sharing}reference collections

DEI, ITB 4

Outline

– common problems in scientific writing (papers, thesis, dissertation)

– common mistakes in writing

– the proposed tools and solutions

– 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

common problems in scientific writing

● Don't know where to {start}.

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

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

common problems in scientific writing (papers, thesis, dissertation)

● Don't know how to give credits

{cite} for informations.

common mistakes in writing

● {Non-flowing} structure and/or story

● {Misplaced} component

● {Bad} referencing/citing

the tools and proposed solutions

● Start from the end

{Bibliography}

● Use a

{reference management system}

● Keep a {log book} or binder

● Keep a {digital} log book or binder

● Use the appropriate {apps}

– Zotero[2], Mendeley[3], Docear[4], JabRef[12], BibDesk[13], etc

– EndNote[5]

● Use the appropriate {apps}

– Evernote[6], – GrowlyNote[7],– Ms OneNote[8]

19 January 2015

DEI, ITB 3

Outline

– common problems in scientific writing (papers, thesis, dissertation)

– common mistakes in writing

– the proposed tools and solutions

– 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}

{Sharing}reference collections

How does it {help}

● {Get} ideas

How does it {help}

● {Choose} ideas

How does it {help}

● {Formulate} ideas

How does it {help}

● {Keep track} of your ideas

How does it {help}

● Build one of multiple {digital} library(ies) and reading list(s)

How does it {help}

● Organize your {pdfs}

How does it {help}

● Based on {topics/ideas}

what are the tools needed

● {Apps:} Reference/citation manager

● We will use {Zotero}[2]

● Read also: Wikipedia[11]

what are the tools needed

● {database/index}: Reference/citation manager

● We will use {Scopus}[10]

● Read also: Wikipedia[11]

Dasapta Erwin Irawan 1

19 January 2015

Reference management A mini course 2_1_1

Outline

● Publishers:

– ResearchGate,

– Academia,

– ResearchID.

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}

account

– Go to alert

– Create alert

Where to {find}

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/

– 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

– 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

Reference management A mini course_2_1_2

Outline

● Publishers:

– ResearchGate,

– Academia,

– ResearchID.

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?

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

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

Reference management 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

Welcome to Zotero

Some terms

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 subtopic

Screen Shot 2015-01-19 at 5.50.25 AM.png

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

a library

How to add a new item/paper

Manually Menu > New Item

Automatic mode: Menu > Import

Select the bib file

There's your item

Automatic mode: Entering the DOI/ISBN

Note the DOI from this paper

How to attach pdf

Attach button

Attach options

How to add some notes

You can add some notes/ paraphrase here

Here's your notes/ paraphrase

How to choose CSL

Here's you CSL pref window

What is CSL (Wikipedia)

The CSL creates this

Zotero's CSL library, search, and download

Installing new CSL file

Here's your new CSL

How to find something

Search window

How to export your doc

Export your entire library

Export your collection

Select your format

How to sync your library

Here's your "sync" button

This is why you need to make an acc

How to connect to Firefox: store info directly from Firefox

Install the add-on first

Enter your keyword

This is your results

Zotero detects the available results, select

Zotero saving the docs, in the cloud

Here's your cloud library

Don't forget to sync

How to connect LO and MSW with Zotero

Left is MsW, right is LO

Adding citation

Adding bibliography

Changing style

Style changed

How to connect LO and MSW with Zotero

Left is MsW, right is LO

Adding citation

Adding bibliography

Changing style

Style changed

Reference Management Course 2015: Complete Materials

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