Table 1.
Dictionaries used in DES-ROD with data source references.
| Dictionary | Enriched unique terms in the KB | Source |
|---|---|---|
| Chemicals/compounds | ||
| Chemical Entities of Biological Interest (ChEBI) [83] | 19,298 | Preexisting in DES |
| Toxins (T3DB) [84] | 2,193 | Preexisting in DES |
| Lipids (lipid maps) [85,86] | 3,099 | Preexisting in DES |
| Amyloids (Human and Mouse), compiled in-house | 394 | Newly compiled |
| Functional annotation | ||
| Biological Process (GO) [87] | 5,868 | Preexisting in DES |
| Cellular Component (GO) [87] | 1,284 | Preexisting in DES |
| Molecular Function (GO) [87] | 1,963 | Preexisting in DES |
| Pathways (KEGG [88], Reactome [89], UniPathway [90], and PANTHER [91]) | 1,584 | Preexisting in DES |
| Diseases | ||
| DOID Ontology (BioPortal) Human Disease Ontology [92] | 3,637 | Preexisting in DES |
| ADO Ontology (BioPortal) Alzheimer's Disease Ontology [93] | 937 | Newly compiled |
| DMTO Ontology (BioPortal) Diabetes Mellitus Treatment Ontology [94] | 1,980 | Newly compiled |
| HFO Ontology (BioPortal) Heart Failure Ontology [95] | 1,002 | Newly compiled |
| CVDO Ontology (BioPortal) Cardiovascular Disease Ontology [96] | 49 | Newly compiled |
| HP Ontology (BioPortal) Human Phenotype Ontology [97] | 3,306 | Preexisting in DES |
| UBERON Ontology (BioPortal) Uber Anatomy Ontology [98] | 6,657 | Newly compiled |
| ICD9 Ontology (BioPortal) International Classification of Diseases, Version 9-Clinical Modification [99] | 719 | Preexisting in DES |
| Drugs | ||
| Drugs (DrugBank) [100] | 4,025 | Preexisting in DES |
| ATC Ontology (BioPortal) Anatomical Therapeutic Chemical Classification [101] | 2,008 | Newly compiled |
| CSSO Ontology (BioPortal) Clinical Signs and Symptoms Ontology | 206 | Newly compiled |
| SIDER (Drug Indications and Side Effects) [102] | 3,203 | Preexisting in DES |
| Human | ||
| Human Genes and Proteins (EntrezGene) [103] | 22,896 | Preexisting in DES |
| Human Transcription Factors [104] | 1,565 | Preexisting in DES |
| Human Transcription Cofactors (TcoF-DB) [104] | 388 | Preexisting in DES |
| Human microRNAs (HGNC [105] and EntrezGene) [106] | 2,088 | Updated |
| Human Long Noncoding RNAs (HGNC) [105] | 527 | Preexisting in DES |
| Mutations (tmVar) [107] | 15,852 | Preexisting in DES |
| Human Anatomy (in-house compiled) | 2,569 | Preexisting in DES |
| OMIT Ontology (BioPortal) Ontology for MicroRNA Target [19] | 695 | Newly compiled |