Comprehensive Assessment of OCR Tools for Gene Name Recognition in Biological Pathway Figures

Optical Character Recognition (OCR) is becoming more and more effective in text detection in images. However, OCR’s performance in special applications may vary. In particular, OCR in visual representations of complex processes known as pathway figures in the biomedical literature is challenging. The information depicted in a pathway graphic usually represents the article’s most important conclusions. Still, the huge number of pathway figures cannot be automatically processed for large-scale search, data mining, and downstream analysis. Assisted by recent developments in OCR, we have developed a method to extract gene names from pathway images. For usage in the method, we thoroughly evaluated and compared major available OCR tools using 563 genes from 45 pathway images, 1000 images of alphanumeric characters and gene names from HUGO, and KEGG data with 20 random pathway genes curated routes. Our study showed that Google Cloud Vision and MMOCR are best suitable for gene name recognition in pathway figures.