A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Table 1

Omics and biomedical applications.

	Omics	Study topic	Biomedical applications
Genetics/molecular genetics	Genomics	Genes	Gencode, Entrez Gene
	Epigenomics	Epigenetics modifications	Gene Express Omnibus
	Exposomics	Disease-causing environmental factors	Comparative Toxicogenomics Database
	Exomics	Exons in a genome	ICE—a human splice sites database
	ORFeomics	Open Reading Frame (ORF)	—
	Phenomics	Phenotypes	Human Phenotype Ontology
	Pharmacogenomics	Impact of genes on individual’s response to drugs	PharmGKB
	Pharmacogenetics	SNPs and their impact on pharmacodynamics and pharmacokinetics	PharmGKB
	Toxicogenomics	Genes response to toxic substances	Comparative Toxicogenomics Database
Molecular biology	Proteomics	Proteins and amino acids	Proteomics Identifications Database (PRIDE)
	Metabolomics	Metabolites	HMDB: Human Metabolome Database
	Transcriptomics	Transcripts (i.e., rRNA, mRNA, tRNA, and microRNA)	Human Transcriptome Map
	Ionomics	Inorganic biomolecules	—
	Kinomics	Protein kinases	KinBase database and KinWeb database
	Metagenomics	Genetic material from multiple organisms	MG-RAST
	Regulomics	Transcription factors and other biomolecules involved in the regulation of gene expression	miRegulome
	Toponomics	Cell and tissue structure	—
Medicine	Trialomics	Human interventional trials from clinical trials	—
	Connectomics	Structural and functional connectivity in brain	—
	Interactomics	Interferons	CREDO

list shows example applications.