Table 2.
Automation tools and software currently used in the systematic review of animal data workflow
| Preclinical systematic review stage | Tool/software | Links to resource or reference |
| Protocol | SYRCLE Protocol | Publication and template51 |
| Systematic search | APIs 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 libraries | ASySD—Automated Systematic Search Deduplication | Code and web application, validation28 29 |
| Citation screening (title and abstract) |
SyRF platform supported by machine learning classification algorithms | 21 23 24 |
| Full-text retrieval | Unpaywall API Reference Manager Software (Endnote or Zotero) (Manual) |
Unpaywall, SCR_016471 Zotero, (SCR_013784) integration with unpaywall EndNote, (SCR_014001), find full-text function ($) |
| Citation screening (Full text) |
SyRF platform | Systematic Review Facility (SCR_01890721) |
| Metadata extraction | Custom Regular Expression Dictionaries | Regular Expression Dictionaries for document tagging and grouping22 54 |
| Risk of bias | Automated detection of blinding, randomisation, and sample size calculation | Text-mining tools for automated detection22 55 CAMARADES Quality Checklist19; SYRCLE’s Risk of Bias Tool56 |
| Data extraction | Machine-assisted data extraction from graphs SyRF for manual data entry, standardised forms for extracting study design characteristics, risk of bias, and quantitative outcome data |
Graph2Data (34) Systematic Review Facility, (SCR_01890721) |
| Meta-analysis | SyRF Meta-Analysis App | Meta-analysis animal data in SyRF Meta-Analysis App18 25 |
| GRADE, SR reporting and publication | GRADE Preclinical certainty of evidence Reporting (CAMARADES appraisal checklist, PRISMA) PRISMA Flowchart generator |
GRADE Preclinical10 Guidelines for reporting systematic reviews and meta-analyses of animal studies.7 PRISMA for preclinical studies under development57 Systematic Review Flowchart generator58 |
| Visualising findings and dissemination | Preprint of SR on Metarxiv Dashboards in Shiny R – custom created for each SR output Interactive Plots in eLIFE and F1000 |
Meta-Research Preprint Server59 R Shiny dashboards60 Interactive Plots with plotly in R61 and integration with publishing platforms, for example, F1000 Interactive Plots62 |
The symbol ‘$’ denotes a paid for software or tool.
PRISMA, Preferred Reporting Items for Systematic Reviews and Meta-Analyses.