Ontogene v2.0: a resource for annotating human genes at transcriptional level with ontologies

In recent years, diverse products of genes in transcriptional level were well investigated, such as protein-coding gene (PCG), miRNA, lncRNA, circRNA, and so on. Their roles that vary from molecule to phenotype in human body attracted much attention these years. Now the annotation of genes’ roles using normalized terminologies is urgent for quantitative analyses. To this end, multiple manually curated databases were established about the annotation of an individual type of roles for an individual type of gene, such as miRNA-disease annotation (HMDD), lncRNA-disease annotation (LncRNADisease), circRNA-disease annotation (CircRNA2Disease), GOA, and so on. Although GeneRIF documented multiple roles of genes in the ‘functional description’ section, these roles were not normalized to ontologies. In summary, there is no online repository for annotating biological roles of genes comprehensively using ontogoies except for Ontogene.

Current functions:

• Asearch: for querying functional annotations of genes by inputting functional terms or genes (miRNAs, lncRNAs, and so on.).
• Glink: for querying gene-term-term-gene path based on gene functional annotation resource and term associations of PubMed.
• Tlink: for querying term-gene-gene-term path based on gene functional annotation resource and gene interaction.
• Web service: for querying the prioritization scores of disease-miRNA associations.
• Submit: for submitting novel functional associations of human genes.

Potential applications:

• Establishing functional association network of genes and their roles.
• Calculating relative score between roles of genes.
• Calculating relative score between genes.
• Predicting novel roles of genes before experimental validation.

Entries		1,548,917
Genes	protein-coding gene	18,699
	ncRNA (miRNA, lncRNA)	1,660
	pseudogene	452
	snoRNA	435
	others	589
	total	21,835
Terms	biological process	12,853
	molecular function	4,321
	cell component	1,900
	disease	4,907
	phenotype	7,778
	total	31,759

June 20, 2019, the Ontogene v2.0 was released.

Liang Cheng, Ph. D.
Associated Professor
School of Life Science and Technology
Harbin Medical University, Harbin 150081, China
Mail: liangcheng@hrbmu.edu.cn