Table 1.
List of dictionaries used in DES-ncRNA, with the number of terms that each dictionary contains and the number of statistically significantly enriched normalized terms identified in the analyzed documents.
| Dictionary | # of terms in dictionaries | # of statistically significant terms in documents | Source |
|---|---|---|---|
| Chemicals/Compounds | |||
| Antibiotics | 6,768 | 203 | pre-existing in DES |
| Chemical Entities of Biological Interest (ChEBI) | 164,419 | 3,943 | pre-existing in DES |
| Drugs (DrugBank + Chembl) | 40,131 | 1,563 | updated from Chembl |
| Enzymes (IntEnz) | 29,993 | 1,192 | pre-existing in DES |
| Metabolites (MetaboLights) | 59,569 | 1,139 | pre-existing in DES |
| Toxins (T3DB) | 47,140 | 728 | pre-existing in DES |
| Functional Annotation | |||
| Biological Process (GO) | 27,801 | 2,816 | pre-existing in DES |
| Cellular Component (GO) | 3,842 | 894 | pre-existing in DES |
| Disease Ontology (DO) | 23,553 | 1,701 | pre-existing in DES |
| Molecular Function (GO) | 10,796 | 717 | pre-existing in DES |
| Pathways (KEGG, Reactome, UniPathway, PANTHER) | 9,650 | 896 | pre-existing in DES |
| General | |||
| Drug Indications and Side Effects (SIDER) | 7,058 | 1,382 | Newly compiled |
| Human Anatomy | 7,167 | 1,476 | pre-existing in DES |
| Genes/Proteins/Transcripts | |||
| Human Genes & Proteins (EntrezGene) | 206,179 | 16,214 | pre-existing in DES |
| Human Long Non-Coding RNAs (FARNA) | 176,516 | 230 | Updated |
| Human MicroRNAs (miRBase) | 9,471 | 931 | Updated |
| Human Transcription Factors (TcoF-DB) | 12,280 | 1,273 | Updated |
| Human Transcription Co-Factors (TcoF-DB) | 3,850 | 345 | Updated |
| Mutations (tmVar) | 192,936 | 7,447 | pre-existing in DES |
References for the data sources indicated in Table 1 are as follows: ChEBI,57 DrugBank,66 Chembl,67 MetaboLights,68 IntEnz,69 T3DB,70 Industrially Important EnzymesEC,71,72 GO,73 KEGG,74 Reactome,75 PANTHER,76 UniPathways,77 EntrezGene,56 NCBI Taxonomy,78 KOBAS,79 FARNA,38 mirBase,13 TcoF-DB,80 tmVar,81 SIDER.59