A scalable artificial intelligence platform that automatically finds copy number variations (CNVs) in journal articles and transforms them into a database: CNV extraction, transformation, and loading AI (CNV-ETLAI). (May 2022)

• Record Type: Journal Article
• Authors: Choi, Jongmun; Jeon, Soomin; Kim, Doyun; Chua, Michelle; Do, Synho
• Is Part Of: Computers in biology and medicine. Volume 144(2022)
• Publication Date: 2022-05
• Subjects: Copy number variation -- CNV-ETLAI -- Natural language processing -- Extraction -- Database -- Microarray -- Artificial Intelligence -- Machine Learning; Medicine -- Data processing -- Periodicals; Biology -- Data processing -- Periodicals; 610.285
• DOI: 10.1016/j.compbiomed.2022.105332
• Languages: English
• ISSNs: 0010-4825

Abstract

Abstract: Background: Although copy number variations (CNVs) are infrequent, each anomaly is unique, and multiple CNVs can appear simultaneously. Growing evidence suggests that CNVs contribute to a wide range of diseases. When CNVs are detected, assessment of their clinical significance requires a thorough literature review. This process can be extremely time-consuming and may delay disease diagnosis. Therefore, we have developed CNV Extraction, Transformation, and Loading Artificial Intelligence (CNV-ETLAI), an innovative tool that allows experts to classify and interpret CNVs accurately and efficiently. Methods: We combined text, table, and image processing algorithms to develop an artificial intelligence platform that automatically extracts, transforms, and organizes CNV information into a database. To validate CNV-ETLAI, we compared its performance to ground truth datasets labeled by a human expert. In addition, we analyzed the CNV data, which was collected using CNV-ETLAI via a crowdsourcing approach. Results: In comparison to a human expert, CNV-ETLAI improved CNV detection accuracy by 4% and performed the analysis 60 times faster. This performance can improve even further with upscaling of the CNV-ETLAI database as usage increases. 5, 800 CNVs from 2, 313 journal articles were collected. Total CNV frequency for the whole chromosome was highest for chromosome X, whereas CNV frequency per 1 Mb of genomic length was highest for chromosome 22. Conclusions: We have developed, tested, and shared CNV-ETLAI for research and clinical purposes (https://lmic.mgh.harvard.edu/CNV-ETLAI ). Use of CNV-ETLAI is expected to ease and accelerate diagnostic classification and interpretation of CNVs. Graphical abstract: Image 1