Extracting Zotero's notes

When reviewing the literature, it’s nice to have the notes linked to Zotero references. It would also be great to compare them systematically. The idea would be to have your notes in Zotero so that everyone in the group can access and edit them and create a data file to explore your notes using, for instance, text analysis techniques.

This small package extracts notes from a collection and creates a CSV file that can be easily read using Excel. You only need to specify the collection ID. For instance, if the location of my collection is https://www.zotero.org/groups/2406179/csic-echo/collections/M8N2VMAP, the collection ID would be M8N2VMAP. We also need the Zotero API’s credentials.

To create a clean CSV, notes’ headers would need a suitable separator. The default is #. In this case, the text between headings mustn’t include #. Below an example:

# Research question

Estimates interaction effects between PGS of obesity and cohorts using HRS.

# Data

HRS

# Methods

Uses a HLM whereby they estimate effects of age and cohorts while making the
intercepts and slopes a function of individual factors.

Installation

pip install git+https://github.com/sdaza/zotnote.git

Credentials

You can save your Zotero API credentials in a config.py and load them using import config:

library_id = "0000000"
api_key = "key"
library_type = "group"

Example

Let’s try to extract some notes and read them using Pandas:

import pandas as pd
import config
import zotnote as zn

zn.exportNotes(collection = "M8N2VMAP", 
    library_id = config.library_id, api_key = config.api_key)

Notes saved in zotero-notes.csv

pd.read_csv("zotero-notes.csv")