GBC Biodata Inventory Update

Purpose: Repeat Methods to Provide an Update of the GBC Biodata Inventory

• The GBC Biodata Inventory conducted in 2022 queried articles published in Europe PMC between 2011 and 2021 and used BERT-based methods to classify articles and extract predicted resource names. This update was done with the same methods, including trained models, to identify new biodata resources published in the literature in 2022 and 2023.

Result: 661 New Resources Identified

• The pipeline was rerun for years 2022 and 2023, with 661 new biodata resources found. These are in addition to the 3112 resources found in the original 2022 inventory.
  • file predictions_final_2024-07-12.CSV contain all resources, from 2011-2023

Process:

• Started with original repo: https://github.com/globalbiodata/inventory_2022
  • Repeated ML pipeline using Google Colab via updating_inventory.ipyn (updated by KES for python packages in Colab)
  • Manually reviewed flagged results
    • Completed manual review file: predictions_v6.csv
    • Optional: Use STEP_1_precheck_manual_reviewed.R to check that all flagged IDs have been reviewed with appropriate values
    • Revision to Process
      • Removing strings of special characters that prevented the rest of the pipeline from running
      • Changes resulted in a V2 of Manual Review Process, also in Zenodo at: https://doi.org/10.5281/zenodo.17644392
  • Completed post-processing pipeline

Exploratory Analysis:

• Analyzed countries for 661 new resources
  • STEP_2_analyze_new_resources.R
  • Author affiliation (total occurrences; may be >1 per article)
  • URL geocoordinates
  • Both known to be tricky; augmented with additional packages/scripts for better coverage
    • as is: new_biodata_resources_2024_unaugmented.csv
    • with additional coverage: new_biodata_resources_2024_augmented.csv
      • Top 5 Countries via Author Affiliations:
        • China (373)
        • USA (92)
        • India (60)
        • Canada (21)
        • UK (20)
      • Top 5 Countries via URL Geocoordinates:
        • China (141)
        • USA (138)
        • India (33)
        • Germany (17)
        • Canada (12)
      • Notes on augmentation
        1. Provision of input files and scripts allows for reproducibility but these scripts will not be generalizable for future updates! Data and code must be reviewed/edited for any future updates to ensure countries are not missed, etc.
      • Plotted maps (jpegs) using new_biodata_resources_2024_augmented.csv