Deus ex machina tool - Confusion matrix computation analyses

Deus ex machina tool - Confusion matrix computation analyses <br> The <em>Deus ex machina</em> code is available on GitHub via this link: https://github.com/code56/ontologiesreproducibility.git Briefly, the code performs semantic annotations on PDF articles and their associated ArrayExpress XML files and computes a Reproducibility Metric Score (RMS) based on various assessment parameters. The case studies are in the field of wheat crop transcriptomics. The accuracy of the Deus ex machina tool of correctly annotating the Plant Ontology terms within wheat transcriptomic articles, was assessed by comparing the manually annotated results and the automatically annotated results, produced by the Deus ex machina tool, with the help of a confusion matrix. The Excel file has 3 tabs that show in detail all the computation analyses (manual annotation of the papers) and the automatic annotation results by the Deus ex machina tool. Some terms were not possible to assign a specific ontology term with confidence (this is the issue where authors did not clarify the terms and describe their research using standardised ontology terms), and these terms are denoted clearly in the computation analysis file. Nonetheless, as the terms were only a few, they do not affect the results of the confusion matrix to any significant degree.