Publications

Abstract
Genes strictly regulate the development of teeth and their surrounding oral structures. Alteration of gene regulation leads to tooth disorders and developmental anomalies in tooth, oral, and facial regions. With the advancement of gene sequencing technology, genomic data is rapidly increasing. However, the large sets of genomic and proteomic data related to tooth development and dental disorders are currently dispersed in many primary databases and literature, making it difficult for users to navigate, extract, study, or analyze. We have curated the scattered genetic data on tooth development and created a knowledgebase called ‘Bioinformatics for Dentistry’ (https://dentalbioinformatics.com/). This database compiles genomic and proteomic data on human tooth development and developmental anomalies and organizes them according to their roles in different stages of tooth development. The database is built by systemically curating relevant data from the National Library of Medicine (NCBI) GenBank, OMIM: Online Mendelian Inheritance in Man, AlphaFold Protein Structure Database, Reactome pathway knowledgebase, Wiki Pathways, and PubMed. The accuracy of the included data was verified from supporting primary literature. Upon data curation and validation, a simple, easy-to-navigate browser interface was created on WordPress version 6.3.2, with PHP version 8.0. The website is hosted in a cloud hosting service to provide fast and reliable data transfer rate. Plugins are used to ensure the browser’s compatibility across different devices. Bioinformatics for Dentistry contains four embedded filters for complex and specific searches and free-text search options for quick and simple searching through the datasets. Bioinformatics for Dentistry is made freely available worldwide, with the hope that this knowledgebase will improve our understanding of the complex genetic regulation of tooth development and will open doors to research initiatives and discoveries. This database will be expanded in the future by incorporating resources and built-in sequence analysis tools, and it will be maintained and updated annually.

URL for Full Article: https://doi.org/10.1371/journal.pone.0303628

Abstract
Objectives: Dental students study the genetics of tooth and facial development through didactic lectures only. Meanwhile, scientists’ knowledge of genetics is rapidly expanding, over and above what is commonly found in textbooks. Therefore, students studying dentistry are often unfamiliar with the burgeoning field of genetic data and biological databases. There is also a growing interest in applying active learning strategies to teach genetics in higher education. We developed a secondary database called “Genetics for Dentistry” to use as an active learning tool for teaching genetics in dentistry programs. The database archives genomic and proteomic data related to enamel and dentin formation.

Methods: We took a systematic approach to identify, collect, and organize genomic and proteomic tooth development data from primary databases and literature searches. The data were checked for accuracy and exported to Ragic to create an interactive secondary database.

Results: “Genetics for Dentistry,” which is in its initial phase, contains information on all the human genes involved in enamel and dentin formation. Users can search the database by gene name, protein sequence, chromosomal location, and other keywords related to protein and gene function.

Conclusions: “Genetics for Dentistry” will be introduced as an active learning tool for teaching genetics at the School of Dentistry of the University of Alberta. Activities using the database will supplement lectures on genetics in the dentistry program. We hope that incorporating this database as an active learning tool will reduce students’ cognitive load in learning genetics and stimulate interest in new branches of science, including bioinformatics and precision dentistry.

URL for Full Article: https://doi.org/10.4258/hir.2022.28.4.387