CommunityData:Zotero: Difference between revisions

Revision as of 17:03, 25 July 2017

We use Zotero for citation management!

Install Zotero

We recommend installing Zotero on your desktop as well as the "connector" for your browser. You can download the software and browser plugin (for Chrome, Firefox or Safari) from the zotero website. You'd also want to register for an account if you don't already have one.

If you were using Zotero before, you should upgrade to Zotero 5.0. You will need to download this from https://www.zotero.org because it was released recently and its not in the distributions yet. It's important to be running the new version. This will break support for BetterBibLaTeX but is also fixes most of the bugs that required this in the first place.

Group Directory

We have a group directory that we use to collect citations for all shared projects: the Community Data Science Collective Zotero repository.. The directory is private, so ask a member of the collective to invite you. The directory is organized by collections (visualized), with each folder aggregating citations for a particular project or topic.

Adding and Organizing References

The process to add something cleanly is complicated but should always include the following steps:

Sync your local Zotero repository (by clicking the little green symbol that looks like a recycle sign in the top right). This may not be necessary all the time, but it's better to do it!
Check to see if it's in the CDSC shared folder by clicking on the top level of the shared group and searching. If it is already there, just drag it into your new subfolder for your project. If it's not, click back on your sub-folder and add it.
Once you've added, change the title to sentence case. You can do this by: (a) Right clicking on Title → Transform Text → Sentence Case (b) you will then need to capitalize any proper nouns (e.g., Scratch, Wikipedia) as well as anything immediately following a ":". This is important because software like BibTeX/BibLaTeX can change from "Sentence case" to "Title Case" automatically, but not the other way around. APA 6 requires sentence case.
Ensure that there's a DOI for your entry if it's necessary. Some publishers and conferences (like AAAI publications which publishes ICWSM) do not have DOIs but these are extremely rare. If your publication does not have a DOI, it needs to have a URL because APA 6 requires one or the other.
Edit & clean the Publisher field. According to APA 6 style we should drop common words like "Press," "Publisher," "Inc." as well as first names (i.e., just Wiley, not John Wiley Inc.)
Edit & clean the Place field. APA 6 style requires "City, State" within the USA and "City, Country" outside. So, it's "New York, New York" for the ACM and "Cambridge, UK" for University of Cambridge Press.
Remove anything in the "Extra" field unless it's something you want to be printed every time. Sometimes things like "ⓒ JSTOR" sneaks in.
Make sure that there's a PDF attached and then rename the PDF to Name-YYYY-Short_title.pdf. You can do this by: Right click on PDF → Rename File from Parent Metadata
Ensure that there aren't extraneous files attached. Just delete anything that doesn't look critical or useful. Keep in mind that anything attached will show up in fulltext searches which can be a reason to either leave something or remove it depending on what it is.

Tips and Tricks

In Zotero, folders are not like traditional folders. They are like tags. Do not add things if they are already there!
Holding down Alt is extremely useful! It will show you which folders the selected item is in!
When you're done adding a bunch of things, look at the Duplicate pseudo-folder underneath the Community Data Science Collective folder.

Exporting

If you want to create a BibTex file from the citations in your folder, right-click your folder in the desktop application, and click "Export Collection". Select BibLaTeX as the format and save to a location of your choice. Be sure to rename the file refs.bib so that it works with the paper-building workflow.

You'll need make, our TeX setup to make this work.

If you are using the latest versions of mako's templates[1] you should be using BibLaTeX.

You should see these lines:

\usepackage[natbib=true,style=apa,backend=biber]{biblatex}

\addbibresource{refs.bib}

That should be it! You should be ready to go! Test it out by running. make refs.bib and make pdf

@@ Line 1: / Line 1: @@
-We use Zotero for citation management.
+We use Zotero for citation management!
 == Install Zotero ==
-We recommend installing Zotero on your desktop as well as your browser. You can download the software and browser plugin (for Chrome, Firefox or Safari) from [https://www.zotero.org/ the zotero website]. You'd also want to register for an account if you don't already have one.
+We recommend installing Zotero on your desktop as well as the "connector" for your browser. You can download the software and browser plugin (for Chrome, Firefox or Safari) from [https://www.zotero.org/ the zotero website]. You'd also want to register for an account if you don't already have one.
+If you were using Zotero before, you should upgrade to Zotero 5.0. You will need to download this from https://www.zotero.org because it was released recently and its not in the distributions yet. It's important to be running the new version. This will break support for BetterBibLaTeX but is also fixes most of the bugs that required this in the first place.
 == Group Directory ==
-We have a group directory that we use to collect citations for all shared projects. The directory is private, so ask a member of the collective to invite you.
+We have a group directory that we use to collect citations for all shared projects: [https://www.zotero.org/groups/163394/community_data_science_collective the Community Data Science Collective Zotero repository].. The directory is private, so ask a member of the collective to invite you.
+The directory is organized by ''collections'' (visualized), with each folder aggregating citations for a particular project or topic.
-The directory is organized by folder, with each folder aggregating citations for a particular project or topic.
-== Exporting ==
+== Adding and Organizing References ==
-If you want to create a BibTex file from the citations in your folder, right-click your folder in the desktop application, and click "Export Collection". Select BibTex as the format and save to a location of your choice. Be sure to rename the file <code>refs.bib</code> so that it works with the [[CommunityData:Build papers|paper-building workflow]].
+The process to add something cleanly is complicated but should always include the following steps:
+# Sync your local Zotero repository (by clicking the little green symbol that looks like a recycle sign in the top right). This may not be necessary all the time, but it's better to do it!
+# Check to see if it's in the CDSC shared folder by clicking on the top level of the shared group and searching. If it is already there, just drag it into your new subfolder for your project. If it's not, click back on your sub-folder and add it.
+# Once you've added, change the title to sentence case. You can do this by: (a) ''Right clicking on Title → Transform Text → Sentence Case'' (b) you will then need to capitalize any proper nouns (e.g., Scratch, Wikipedia) as well as anything immediately following a ":". This is important because software like BibTeX/BibLaTeX can change from "Sentence case" to "Title Case" automatically, but not the other way around. APA 6 requires sentence case.
+# Ensure that there's a DOI for your entry if it's necessary. Some publishers and conferences (like AAAI publications which publishes ICWSM) do not have DOIs but these are extremely rare. If your publication does not have a DOI, it needs to have a URL because APA 6 requires one or the other.
+# Edit & clean the Publisher field. According to [http://blog.apastyle.org/apastyle/2010/01/the-generic-reference-where.html APA 6 style] we should drop common words like "Press," "Publisher," "Inc." as well as first names (i.e., just Wiley, not John Wiley Inc.)
+# Edit & clean the Place field. [http://blog.apastyle.org/apastyle/2010/01/the-generic-reference-where.html APA 6 style] requires "City, State" within the USA and "City, Country" outside. So, it's "New York, New York" for the ACM and "Cambridge, UK" for University of Cambridge Press.
+# Remove anything in the "Extra" field unless it's something you want to be printed every time. Sometimes things like "ⓒ JSTOR" sneaks in.
+# Make sure that there's a PDF attached and then rename the PDF to ''Name-YYYY-Short_title.pdf''. You can do this by: ''Right click on PDF → Rename File from Parent Metadata''
+# Ensure that there aren't extraneous files attached. Just delete anything that doesn't look critical or useful. Keep in mind that anything attached will show up in fulltext searches which can be a reason to either leave something or remove it depending on what it is.
-== Zotero Better Bibtex Extension ==
+== Tips and Tricks ==
-Better Bib(la)tex [https://github.com/retorquere/zotero-better-bibtex] is a useful extension for using zotero with [[CommunityData:TeX|Tex]].
-Better BibTeX has a few nice features:
+* In Zotero, folders are not like traditional folders. They are like tags. Do not add things if they are already there!
-# It supports BibLaTeX which supports Unicode better than regular BibTeX
+* Holding down <tt>Alt</tt> is extremely useful! It will show you which folders the selected item is in!
-# Automatic journal abbreviations.
+* When you're done adding a bunch of things, look at the ''Duplicate'' pseudo-folder underneath the ''Community Data Science Collective'' folder.
-# No longer need refsprocessed.bib
-# Automatically syncing .bib files with zotero collections
-# Pulling .bib files from zotero with an http request
+== Exporting ==
-This final feature is particularly useful if you are [[CommunityData:Build papers|building papers]] with make.
+If you want to create a BibTex file from the citations in your folder, right-click your folder in the desktop application, and click "Export Collection". Select BibLaTeX as the format and save to a location of your choice. Be sure to rename the file <code>refs.bib</code> so that it works with the [[CommunityData:Build papers|paper-building workflow]].
-Let's walk through steps for setting up Better BibTeX with make.
-=== Setup Better BibTeX with Make ===
-You'll need make, our [[CommunityData:TeX|TeX]] setup and wget to make this work.
-==== Installing and Configuring Better BibTeX ====
-# Install from instructions on github https://github.com/retorquere/zotero-better-bibtex/wiki/Installation
-# Open Zotero preferences, go to the Better BibTex tab
-# Open export subtab (under Better BibTeX) and enable "Enable export by HTTP". This turns on an HTTP server that can export your Zotero collections.<br/>Note: This step is not needed if using Zotero Standalone, as it always runs the server.
-# Open the Automatic export subtab and select "Disabled".
-The below steps may not be necessary, but they help getting cleaner bib files that won't add much strange junk you your bibliography.
-*  add "keywords,note,abstract,eprint,isbn,rights,issue" to the "Fields to omit from export(comma-separated) field. If any of your zotero entries start adding weird crap to your bibliography you can stop it using this setting.
-* I also select DOI for "When a reference has both DOI and an URL, export
-There are many other Better BibTeX settings, but the above are the ones that I think are useful for use with make.
-==== Make sure your Tex file is using BibLaTeX ====
+You'll need make, our [[CommunityData:TeX|TeX]] setup to make this work.
 If you are using the latest versions of mako's templates[http://projects.mako.cc/source/?p=latex_mako] you should be using BibLaTeX.
@@ Line 57: / Line 46: @@
 \addbibresource{refs.bib}
 </code>
-If you aren't using Better BibTeX I suggest merging your document with Mako's template so that you are using the bibliography setup from the template.
-==== Modifying Makefile to use your Zotero Collection ====
-Make a few small changes to Makefile in paper_template.tex so running make synces refs.bib to your Zotero collection.
-g
-# Identify the url you can use to download your Zotero Collection.
-## Right click on the collection and then click on BibLaTeX url.
-## There may be two urls show. It is better to use the one derived from the name of the collection since it should be the same for everyone. it has a unique identifier. It looks like this: http://localhost:23119/better-bibtex/collection?/1233037/<COLLECTION_NAME>.biblatex.
-## Copy this url
-# Test that the url works by opening it in your browser. You should see your .bib file! You may have to change how whitespace is represented for example by replacing %20 with '\ '.
-# Now modify the Makefile to download the file and output it to refs.bib. Add these two lines:<br /><code>refs.bib: <br/><TAB> wget -r -q -O refs.bib "your_collection_url"</code> <br/>
-# Next add refs.bib to the dependencies of .tex. Add <code>refs.bib</code> to the end of the line that starts with <code>%.tex:</code>
-# Finally make refs.bib phony so that you update refs.bib every time you run make. Add <code>refs.bib</code> to the end of the line that starts with <code>.PHONY</code>.
 That should be it! You should be ready to go! Test it out by running.
 <code> make refs.bib </code> and <code> make pdf </code>