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Collecting, organizing and
citing scientific literature:
an intro to Zotero
Mark Dingemanse
Wikimedia Commons
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Collecting, organizing and
citing scientific literature:
an intro to Zotero
Mark Dingemanse
Wikimedia Commons
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Collecting, organizing and
citing scientific literature:
an intro to Zotero
Mark Dingemanse
Wikimedia Commons
#FixedThatForYou
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collecting literature
building a library
citing sources
Core tasks for any scientist
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A common pre-Zotero workflow...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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Typical problems
Heaps of PDFs with inscrutable file names
No links between metadata, files, notes
When citing, copy+paste best option
Hard to share papers with metadata
Pointless reformatting of references
Collaboration difficult to organise
...
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collecting literature
building a library
citing sources
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collecting literature
building a library
citing sources
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collecting literature
building a library
citing sources
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collecting literature
building a library
citing sources
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Install Zotero from zotero.org
zotero.org/download
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I
Collecting literature
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Whatever the scenario
locating a specific paper
open-ended literature search
your search probably starts online
with services like Google Scholar, PubMed,
ScienceDirect, Web of Science, etc.
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Suppose this is the one your
were looking for; click it
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Zotero has detected something
it can save to your library
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One click does it — including
the PDF if you have access
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Be picky about metadata quality
Use Google Scholar to quickly find stuff
but try to go to an article’s own page to save it
Use DOIs when you can
they point to the article’s official location
Zotero can easily import them
Rules of thumb
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Be picky about metadata quality
Use Google Scholar to quickly find stuff
but try to go to an article’s own page to save it
Use DOIs when you can
they point to the article’s official location
Zotero can easily import them
Rules of thumb
Why? Google Scholar is often incomplete (e.g.
no abstract, no DOI, etc.) — invest up front in
high quality metadata and never look back
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Be picky about metadata quality
Use Google Scholar to quickly find stuff
but try to go to an article’s own page to save it
Use DOIs when you can
they point to the article’s official location
Zotero can easily import them
Rules of thumb
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Be picky about metadata quality
Use Google Scholar to quickly find stuff
but try to go to an article’s own page to save it
Use DOIs when you can
they point to the article’s official location
Zotero can easily import them
Rules of thumb
DOI (digital object identifier) is like a unique
address for every scientific document. A DOI
also makes a link: just type “doi.org/” before it
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While you’ll usually add new papers from within the
browser, Zotero is pretty good at dealing w/ PDFs
drag into your library to automatically retrieve
metadata (success rate depends on age & type)
Zotero will store a copy, rename it, index it for
search, and sync it (if file syncing is enabled)
if auto-import fails, Zotero will let you add metadata
using DOI, via a good repository, or manually
Importing PDFs
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Zotero senses when you’re looking
at a single vs multiple papers
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It can also save multiple papers at
once (think systematic review)
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In addition to direct import from hundreds
of journals & repos, Zotero supports:
Save from almost any library catalog
Import via DOI, ISBN or PMID
Import from RIS, BibTex, etc.
(If all else fails:) manual entry
Other methods
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Other methods
The whole point of Zotero is
that it automates grunt work to
let you focus on real work.
In addition to direct import from hundreds
of journals & repos, Zotero supports:
Save from almost any library catalog
Import via DOI, ISBN or PMID
Import from RIS, BibTex, etc.
(If all else fails:) manual entry
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II
Building a library
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Wikimedia Commons
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offers multiple ways of browsing/searching
has complete and definitive metadata
makes studying & note-taking easy
A good library
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collections library reference pane
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settings add & export search sync
collections library reference pane
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tags
settings add & export search sync
collections library reference pane
notes
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Collections and tags
Searching
Notes
Zotero basics
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Collections
most like your old-school paper filing system
papers can be in multiple collections
most useful for coherent projects
Tags
flexible cross-categorisation by keyword
most useful for tagging topics or methods
or for workflow management (*need to read &c)
Collections vs Tags
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As your library grows, you’ll find yourself
preferring search over collections & tags
Z can search metadata but also fulltext PDFs
Basic search is fast, advanced search flexible
Searches can be saved for dynamic updates
Saved searches are useful
‘all items added in last month’
‘all books w/ PDFs’
Search
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Notes can be your external memory
What are the key points of this paper?
Do I ever want to read this again?
What was that clever phrasing?
Notes
Protip: if you read/annotate on other
devices, the ZotFile plugin can import
your PDF annotations & highlights
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Example: using Tags+Notes to record memorable quotes
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Example: using Tags+Notes to record memorable quotes
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Example: using Tags+Notes to record memorable quotes
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III
Citing sources
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Culumber et al. 2014, Ethology [since corrected]
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Citing sources is a double-edged sword
attribution — giving credit where credit is due
selection — separating wheat from chaff
Citing sources is not:
wasting your time changing initials to full names,
commas to colons, or other pointless things
That’s what Zotero is for.
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Citing sources is a double-edged sword
attribution — giving credit where credit is due
selection — separating wheat from chaff
Citing sources is not:
wasting your time changing initials to full names,
commas to colons, or other pointless things
That’s what Zotero is for.
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Installing Zotero will add new Z
toolbar to your word processor
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Clicking ‘Add/Edit’ brings up a
fast and user-friendly search bar
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In-text citations
counting authors, switching to et al. when needed
adding a,b for papers by same author, same year
using numbered or alphabetic styles ...and much more
Bibliography
ensuring everything cited is in bibliography
following even the most arcane formatting rules
fixing indentation, capitalization ...and much more
Features
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switching between styles is trivially easy
8000+ styles at zotero.org/styles
styles can be edited if needed
Styles
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Go to zotero.org/styles
Find your desired citation style
Click it
Add styles via zotero.org/styles
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Go to zotero.org/styles
Find your desired citation style
Click it
Add styles via zotero.org/styles
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IV
Advanced topics
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Synchronizing & backing up
Where your files go
Importing PDFs
Group libraries
Plugins
Advanced topics
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Local storage
Zotero stores
metadata & notes in a local database
PDFs & other attachments in /storage/
citation styles in /styles/
Zotero Storage directory
by default in your user profile
easy to move elsewhere
(do so for ‘roaming profiles’ on Windows)
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Zotero stores
metadata & notes in a local database
PDFs & other attachments in /storage/
citation styles in /styles/
Zotero Storage directory
by default in your user profile
easy to move elsewhere
(do so for ‘roaming profiles’ on Windows)
Local storage
a large Zotero library in a roaming
profile may slow down user login
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Zotero can synchronise across devices
metadata & notes: unlimited
attachments: up to 300Mb for free
use Z on laptop, web, mobile devices
Setting up syncing
1. create Zotero account
2. enter info in Z preferences
Sync
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Zotero can synchronise across devices
metadata & notes: unlimited
attachments: up to 300Mb for free
use Z on laptop, web, mobile devices
Setting up syncing
1. create Zotero account
2. enter info in Z preferences
Sync
Protip: to sync is to back up —
even if you work on one device
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1. Zotero File Storage
Starting from $20/y for 2Gb, 6Gb, unlimited storage
tiers (your institution may reimburse)
2. WebDAV
Freemium (e.g. box.net) or institutional servers can
offer anything between 2Gb and unlimited space
3. Dropbox/Google Drive [workaround]
Not recommended, as database may become
corrupted; see the Zotero forums for workarounds
Sync: Remote storage
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Zotfile: PDF management for Zotero
automatically rename, move, link PDFs
share files with your mobile devices
Zutilo: advanced editing & shortcuts
copy, paste, remove sets of tags
copy and paste in multiple citation formats
Zotero Better BibTex
generate stable citekeys for use in LaTeX/Markdown
push/pull export in background to keep libraries in sync
& many more: zotero.org/support/plugins
Plugins
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Can I use Zotero with BibTex/Latex?
Sure — use the Zotero BetterBibTex plugin
Can I import my messy pile of PDFs?
Sure — drag them into the library to let Zotero
retrieve the metadata for you
Can I import from another reference manager?
Sure — for help, check the Zotero forums
Can I export to other reference managers?
Sure — Zotero doesn’t try to lock you in and makes it
easy to switch or use multiple systems (e.g. BibTex + Z)
Frequently Asked Questions
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collecting literature
building a library
citing sources
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Zotero takes care of everything that makes
you weep and curse when doing it manually
It puts hair-splitting editors out of business
and lets scientists focus on real work
In short
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Zotero is cross-platform, free and open source —
made by scholars for scholars
Users can contribute ideas and code, forming a
rich and healthy plug-in ecosystem
Development is agile and usage-driven, rather
than rigid and profit-driven
There is no profit motive, hence no incentive
for user lock-in & monetization
Openness matters
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Plenty of docs & tutorials on zotero.org
Zotero Forums offer helpful advice
Your librarians can often help
(If all else fails:) drop me an email
Questions?
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Feel free to share, remix, reuse
Licensed under CC BY 4.0 by Mark Dingemanse
follow @DingemanseMark