Table 2

Automation tools and software currently used in the systematic review of animal data workflow

Preclinical systematic review stageTool/softwareLinks to resource or reference
ProtocolSYRCLE ProtocolPublication and template51
Systematic searchAPIs for PubMed
APIs for Web of Science
APIs for biorxiv and medrxiv
Living Search for PubMed
PubMed API (RRID:SCR_013249)
‘wosr’ R package52 medrxivr R package53
SyRF Platform21
Deduplicating reference librariesASySD—Automated Systematic Search DeduplicationCode and web application, validation28 29
Citation screening
(title and abstract)
SyRF platform supported by machine learning classification algorithms21 23 24
Full-text retrievalUnpaywall API
Reference Manager Software (Endnote or Zotero) (Manual)
Unpaywall, SCR_016471
Zotero, (SCR_013784) integration with unpaywall
EndNote, (SCR_014001), find full-text function ($)
Citation screening
(Full text)
SyRF platformSystematic Review Facility (SCR_01890721)
Metadata extractionCustom Regular Expression DictionariesRegular Expression Dictionaries for document tagging and grouping22 54
Risk of biasAutomated detection of blinding, randomisation, and sample size calculationText-mining tools for automated detection22 55
CAMARADES Quality Checklist19; SYRCLE’s Risk of Bias Tool56
Data extractionMachine-assisted data extraction from graphs
SyRF for manual data entry, standardised forms for extracting study design characteristics, risk of bias, and quantitative outcome data
Graph2Data (34)
Systematic Review Facility, (SCR_01890721)
Meta-analysisSyRF Meta-Analysis AppMeta-analysis animal data in SyRF Meta-Analysis App18 25
GRADE, SR reporting and publicationGRADE Preclinical certainty of evidence
Reporting (CAMARADES appraisal checklist, PRISMA)
PRISMA Flowchart generator
GRADE Preclinical10
Guidelines for reporting systematic reviews and meta-analyses of animal studies.7 PRISMA for preclinical studies under development57
Systematic Review Flowchart generator58
Visualising findings and disseminationPreprint of SR on Metarxiv
Dashboards in Shiny R – custom created for each SR output
Interactive Plots in eLIFE and F1000
Meta-Research Preprint Server59
R Shiny dashboards60
Interactive Plots with plotly in R61 and integration with publishing platforms, for example, F1000 Interactive Plots62
  • The symbol ‘$’ denotes a paid for software or tool.

  • PRISMA, Preferred Reporting Items for Systematic Reviews and Meta-Analyses.