Review Article
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.
|