The Mega Meta project: Substance use, anxiety and depression

The Center for Urban Mental Health at the AMC is cooperating with ASReview for an enormous, systematic review and meta-analysis (> 165.046 hits)  to find out what factors and interaction of factors contribute to the onset, maintenance, and relapse of anxiety-, depressive-, and substance use disorders.  

Some highlights:

  • A team of 7 students and researchers screened 11.571 papers in a period of only 5 months!
  • ASReview ran via a server so that everyone could screen at the same time.
  • A part of the literature was also screened using a 17-layer CNN model developed by a former student of the master Applied Data Science, which is pretty cool!
  • For post-processing the results hundreds of lines of code were written: DOI-retrieval, deduplication, merging different files – you name it.
  • The next and ongoing step is data extraction to run some amazing meta-analysis.

All codebooks, search strings, scripts, and much more is published so that anyone can benefit from the work. More details below:

This project is funded by a grant from the Centre for Urban Mental Health, University of Amsterdam, The Netherlands

Research partner ASReview: Centre for Urban Mental Health

Pre-registration

The following PROSPERO pre-registration was created for the MegaMeta project. The pre-registration describes the review question, the types of studies to be included, population, interventions, exposure(s) and much more.

Find the details in the PROSPERO pre-registration:

 

Brouwer, M., Wiers, R., van den Brand, S., Hofstee, L., van de Schoot, R., Bockting, C. (2021). Reviewing factors that contribute to substance use, anxiety and depressive disorders. PROSPERO: CRD42021266297

Pre-registration – Prospero

The search protocol repository contains the procedure for

  1. the search terms,
  2. the search query,
  3. selected key papers,
  4. de-duplication via Endnote.

 

Brouwer, M., Hofstee, L., de Boer, J., Weijdema, F., Lucassen, P., Sloot, P. M. A., Stronks, K., van Weert, J., Wiers, R., van de Schoot, R., & Bockting, C. (2021). Search Protocol for the Mega-Meta Study on Factors Contributing to Substance Use, Anxiety and Depressive Disorders. Open Science Framework. DOI:  10.17605/OSF.IO/M5UHY 

Search protocol – OSF

Screening protocol

The screening protocol repository contains the procedure for screening the records identified in the search protocol.

 

Hofstee, L., Brouwer, M., Melnikov, V., & van de Schoot, R. (2021). Screening Protocol for the Mega-Meta Study on Factors Contributing to Substance Use, Anxiety and Depressive Disorders. Open Science Framework. DOI:  10.17605/OSF.IO/3ZNAR

Screening protocol – OSF

Server Setup

To allow for continuation of the screening project between different screeners, a server was setup. Details on how this server was setup can be found in the GitHub repository, or zenodo publication

 

Melnikov, V. (2021). ASReview server setup for MegaMeta study. Zenodo. DOI:10.5281/zenodo.5768306

Server setup – GitHub

Hyperparameter tuning

This repository stores the scripts and plugins that were used for the creation of three final data files for screening titles and abstract in a second round. These final project files were created using a classifier based on a convolutional neural network, optimized using Optuna.

 

Teijema, J., & Van de Schoot, R. (2021). Hyperparameter-training for the Mega-Meta project. Zenodo. DOI: 10.5281/zenodo.5747050

Hyperparameter tuning – GitHub

Post processing

This repository stores the scripts to post-process the data after the title and abstract screening phase. Post-processing consists of the following steps.

  1. Merge the three output files after screening in ASReview;
  2. Obtain missing DOIs;
  3. Apply another round of de-duplication (the first round of de-duplication was applied before the screening started).
  4. Deal with noisy labels corrected in two rounds of quality checks;

 

van den Brand, S., Hofstee, L., Teijema, J., Melnikov, V., Kramer, B., Brouwer, M., & Van de Schoot, R. (2021). Scripts for Post-Processing Mega-Meta Screening Results. Zenodo. DOI: 10.5281/zenodo.5752358

Post-processing – GitHub