building bibliographies and managing citations with mendeley

Building bibliographies and managing citations with Mendeley

Ada Giannatelli20th March, 2014

METID – Politecnico di Milano

Disclaimer: due to the continuing development of Mendeley, no guarantee for the accuracy of information over time can be assumed

Mendeley in a nutshell

Mendeley is a reference and citation managerFree, not open source. Available for Mac, Windows and Linux

Reference and citation manager = software application that helps gather, organize, and maintain references for your researchExamples (besides Mendeley): EndNote, Zotero

Mendeley in a nutshell

1

Web application

2

Desktop application

3

iOS App + unofficial Android Apps

3

components of

Mendeley:

+

+

Mendeley’s identity card

...backed by co-founders and former executives of:

Supported by:

Startup founded in 2008 and acquired by Elsevier in April, 2013

Based in London, Mendeley at the origin = 30+ researchers, graduates and software developers from...

Why use a reference and citation manager?

How to integrate Mendeley into my workflow?

ONBOARDING

• Sign up to Mendeley web

• Install Mendeley desktop

• Install browser bookmarklet / Word plugin

• Organize existing articles

ROUTINE

• Information gathering

• Information processing

BEFORE

• Papers in digital and paper format

• Papers on multiple devices

• Notes on articles saved only on the device where they were made

Information gathering with Mendeley features

Information gathering

Import existing research with [add file], [add folder]On Mendeley Desktop:

1. [file > add file] or [file > add folder]2. select the file / folder you would like to import. All PDFs will be imported

into Mendeley3. MyLibrary > New folder: additional organization with subfolders that

match e.g. your research topics or courses (drag&drop files, such as PDFs and Words, into the sub folder)


Import new research with [watch folder]On Mendeley Desktop:

1. file > watch folder 2. tick the folders you want mendeley to watch. Any new PDFs in these

folders will be imported into Mendeley automatically (remember to click [apply])


Import new research with [save to Mendeley] bookmarklet supported sites


Import new research with [save to Mendeley] bookmarklet

Mendeley normally bookmarks links and saves

metadata, NOT the corresponding files

Verify that [Details]: if theys look ok, click the

[Save] button


Import new research from ScienceDirect

Information gathering > Search for crowdsourced

papers

Information gathering > Search for crowdsourced papers


Search for crowdsourced papers

Search across the full-text of your library

Sync your data across devices

Double click a document to open in the PDF viewerFilter your papers by authors,

keywords, tags, or publications

See document details to quickly update meta-data and browse notes

Information gatheringSync data across devices / Interface anatomy

contents : e.g.table of contents; enrichments: e.g. figures

Information gathering > Highlight, annotate, add sticky notes

Information processing with Mendeley features

Information processing

Generate bibliographies and citations (Word)

Select the Citation Style you would like to use. Once you have an article open or selected, choose Ctrl + C (PC) to copy the citation. Keep in mind that this is not always perfect – make sure to check your citations!


Generate bibliographies and citations


Generate bibliographies and citations (LaTeX)

1. Open Mendeley Desktop and select the files you wish to export.

2. Go to the File menu and select Export. Save as BibTeX type and save to the same folder that contains your LaTeX files.

3. To create your bibliography in your LaTeX file, enter two commands:\bibliography{yourfilename} where yourfilename refers to the name of the .bib file you exported from Mendeley. This command generates the bibliography.

4. To insert an in-text citation, enter this command:

\cite{__} where __ is the citation key assigned (in the .bib file) to the source you want to cite.


Generate bibliographies and citations (LaTeX)

Mendeley: tips&tricks

Literature search: choose [open access] to perform full-text search

open access

If you use LaTeX to write your articles, Mendeley automatically syncs its database to a nominated .bib file for BibTeX or BibLaTeX with up to date research data

for LaTeX users

If needed (e.g. to clean up “altered” citation keys imported from Papers database into Mendeley), Mendeley Desktop’s local configuration and data store is sqlite, a standard lightweight application storage database (SQL interface)

manual cleaning

Author names with apostrophes, such as “O’Sullivan”, generate invalid citation keys in the .bib file (e.g. “O’Sullivan1990″). You have to perform a manual edit of the citation key in the desktop app (e.g. “OSullivan1990″)

mind apostrophes


Use advanced search operators to narrow down your search results

Search for... ...to find articles that have

citation analysis the words citation or analysis

citation AND analysis both the words citation and analysis

ponies OR "small horses" the word ponies OR the exact phrase small horses

ponies AND -"small horses" the word ponies but NOT the phrase small horses

"real time quantitative PCR" the exact phrase real time quantitative PCR

title:"real time quantitative PCR"the exact phrase real time quantitative PCR in the title field

author:Campbell AND author:Ellis

both the names Campbell and Ellis in their list of authors

published_in:"PLoS Medicine"the exact phrase PLoS Medicine in their journal or publication name

intracellular AND year:2008the word intracellular and were published in the year 2008


Search: gamification and year:2014


My Library SearchOnly available when searching your local library, or groups.


tag:"To read" the tag or keyword To read

note:"study material" contains the exact phrase study material in the notes field.

Literature SearchOnly available when using the "Literature Search" on Mendeley Desktop, or the Paper search on the Mendeley Web.


oa_journal:yes is published in a Journal that Mendeley recognizes as Open Access

intracellular AND year:[1998 TO 2008]

the word intracellular and were published between the years 1998 and 2008

Mendeley: caveat

At the moment Mendeley itself can’t search research databases directly (feature under development), but you have to go to each online article database, search and import each result into Mendeley with the browser bookmarklet

no search across external databases

Mendeley does have a search tool for searching papers that other users have imported into Mendeley. This is helpful if you are in a field that has a lot of Mendeley users (e.g. life science)

crowdsourced papers

Mendeley doesn’t use a standard research taxonomy (e.g. CERCS), but it assigns a “discipline” to a particular paper based on who is reading it

no standard research taxonomy

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Mendeley mobile

iOS App• View the same folder structure

as your Desktop / laptop to easily find files

• Add tags• Highlight and add notes• Once the Mendeley app syncs

with it’s cloud service, you will be able to see your highlights or notes on your Desktop/laptop as well

unofficial Android Apps• Scholarley• Pubchase• …

For more info…

Reference management software comparison (Imperial College London)- Dec, 2013https://workspace.imperial.ac.uk/library/Public/Reference_management_software_comparison.pdf

Mendeley help guides, videos and tutorialshttp://resources.mendeley.com/index.html

https://workspace.imperial.ac.uk/library/Public/Reference_management_software_comparison.pdf

https://workspace.imperial.ac.uk/library/Public/Reference_management_software_comparison.pdf

http://resources.mendeley.com/index.html

http://resources.mendeley.com/index.html

building bibliographies and managing citations with mendeley

Education

file gt

add file

crowdsourced

bib file

add folder

tipsamp

mendeley desktop

find articles