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")
id citation tags title reviewer research_question model data methods conclusions the_good limitations results context next
0 4ESWAPZY van Dijk et al. 2015 NaN Recent developments on the role of epigenetics... Elena Knowledge about epigenetic marks related to ob... Human and animal Review NaN NaN Good summary tables of studies carried out in ... So far, a causal role of epigenetics in the de... NaN NaN NaN
1 5JNF33U8 Fernandez-Twinn et al. 2019 intrauterine effects, epigenetics Intrauterine programming of obesity and type 2... Elena Which are the relevant exposures related to th... Human and also murine models NaN NaN -          The main exposures involved: fetal ... NaN limited evidence for  a causal role for epigen... NaN NaN NaN
2 S8FZS32L Ling 2019 Elena Epigenetics in Human Obesity and Type 2 Diabetes Elena Summarizes epigenetic signatures from human ti... NaN Human Different large-scale methylation studies usin... NaN Also covers diet (methyl donnors) and epigenet... In epigenetic studies it’s important to unders... 1) Evidence for DNA methylation sites that con... NaN NaN
3 QY3Y7V6X Sharp et al. 2017 Must read Maternal BMI at the start of pregnancy and off... Elena Is maternal bmi related with changes in the of... NaN meta-analysis across 19 cohorts using 450k ill... 2 models: primary análisis used continous bmi ... They found evicence for a causal intrauterine ... Large sample size n=7523. Strong confounder co... Effects sizes were very small, les tan a 0.15%... NaN NaN NaN
4 5AMCHQMB Sulc et al. 2020 NaN Quantification of the overall contribution of ... Sebastian Can we use a method to estimate GxE without me... NaN Simulation and application to complex traits f... Detect GxE based on the variance heterogeneity... NaN Interesting approach to GxE and GxG. The metho... The interaction effect estimates may depend to... Simulation results seem to show the method is ... GxE are challenging, E is not measured accurat... What would be the implications of these result...
5 U4MNK7QT Walter et al. 2016 Genomics, HRS, GxE, BMI Association of a Genetic Risk Score With Body ... Sebastian Estimates interaction effects between PGS of o... NaN HRS Uses a HLM whereby they estimate effects of ag... NaN NaN Pays little attention to selection due to surv... NaN NaN Anything
6 RGDC9R9R Abadi et al. 2017 Genomics, GxG, GxE, BMI Penetrance of Polygenic Obesity Susceptibility... Sebastian Are the effects of obesity-susceptibility loci... NaN Several studies, including the Framingham coho... Conditional quantile regression (CQR) to inves... NaN Interesting approach to GxE and GxG. European ancestry, how these results hold in d... Significant positive associations (adjusting f... The role of the individual and compound gene-e... What would be the implications of these result...