Reference and Knowledge Management (Zotero, Qiqqa)

2016 - 07 - 01

see also: ResearchGo:研究生活第一帖——文献检索与管理 王晋东


We need to have 2 parts: a standalone client running in Windows, and a browser extension capturing web page info to send to the client. Besides, we need some zotero extensions to automate bib info and file naming.
Note: Zotero 4 is suggested, Zotero v5 canNOT automatically attach files, we need to do it manually. To disable auto-update in v4, goto advanced > about:config (ref), disable "update"-related options:

Download v4 here.
Download Browser Connecter here. (zotero 5 is not recommended )
( zotero can also import from clip board without using browser connecter)

general settings

extra citation styles

If the wanted styles are not built-in, you can try
E.g. ASCE format
E.g. Chinese GB/T 7714 format

Download .csl files and add via Zotero Preferences.

must-have addons/extensions

Tested with: Zotero Standalone v4 & v5 for Windows.
Notice for firefox users: right click to save as files, do not click directly.

better bibtex:

For Zotero v4, right click here to save v1.6.100.
For Zotero v5, see here.
The suggested cite key format is [auth:lower][year][veryshorttitle:lower] (best practice; used as default by google scholar & qiqqa etc.). The old format ([auth:lower][shortyear]) is dated, and not suggested.
better bibtex
To export, right click a folder/collection or root-folder, choose "better BibTex":


For Zotero v4, right click to save v4.2.8 here.
For Zotero v5, see here.

  • watching a folder makes your life easy (Zotero v4 only)

    zotero watching a folder

  • suggested filename format: {%a}{ %y}{ %t} (so that "everything search (64bit)" can work.)

The pic above, max auth = 1 & suffix (et al.) are not used

  • more advanced settings

use English for GUI

Preferences (首选项) > Advanced (高级) > Open about:config (打开配置编辑器) > Set "intl.locale.matchOS " to "false".

Qualitative Data Analysis (QDA)


Download here.
Qiqqa (pronounced as "quicker") is not exactly a QDA software, but between traditional ref mgmt and QDA. It is free if internet sync needed is less than 500 MB.
A mentor/friend suggested a software Atlas.ti, so I searched as always. Superingly, a thing called Qiqqa has a higher votes than Zotero, but I never heared. Thus, I decided to try Atlas.ti and Qiqqa.
The most interesting thing is inCite. See all tutorial videos here.

important features compared with zotero:

  • OCR, which is useful for search
  • Annotation report
  • Theme & Expendition
  • Integrated Brainstorm

The idea difference between zotero & qiqqa is that, Zotero starts one reference from getting bibtex meta-data, for instance, using chrome plugin. Qiqqa starts with pdf file, and Qiqqa makes it easy to fill in the related bibtex metadata with "sniffer".
From first several days of experience, the efficiency is the same, but it takes some time to get use to different methodology.

how to > init:

  1. export zotero lib with notes & files as bibtex
  2. create qiqqa account, log in
  3. suggested: config > system > max number of OCR processes : (CPU cores - 1)
  4. open my own library (not the guest lib), import from bibtex.bib, the pdf files will also be imported


Qiqqa's "ctrl + F" search & multi-highlighting is shown below:

how to > restore / change computer:

to be cont.
Attention: firstly set: config > system > data directory (leave other directories alone, they will be inside the data dir)


After using Qiqqa for half a year: The best thing in Qiqqa is "annotation report". DO remember to select "doc comments". The generated report is then a very good "paper summary".

I use both Qiqqa and Zotero. The only reason is, Qiqqa did not provide hierarchical organization of papers. I use Zotero for the hierarchical structure (see pic below) and use "ctrl+shift+c" to copy metadata from Zotero and paste into Qiqqa.

Another issus is the highlighting is behaving in a different way that we get used to. A tip is, if we highlight the same text 2nd time, we can erase the highlights.

related software

See QDA for content management.

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