Table 1 Associations between graph entities and biological information
From: BioGraph: a web application and a graph database for querying and analyzing bioinformatics resources
Type | Label | # | Biological information | Source |
|---|---|---|---|---|
Nodes | Gene | 59839 | Genes | NCBI entrez genes |
| Â | Go | 43969 | Functional annotations | Gene ontology |
| Â | Protein | 20193 | Proteins | UniProtKB |
| Â | Pathway | 1920 | Pathways | Reactome |
| Â | MiRNA | 28645 | miRNA precursors | miRBase |
| Â | MiRNAmature | 38558 | miRNA matures | miRBase |
| Â | MiRNAsnp | 236 | miRNA SNPs | miRNASNP |
| Â | Cancer | 107 | Cancers | mirCancer |
| Â | ProteinName | 219132 | Proteins accessions | UniProtKB |
| Â | GeneName | 115027 | Genes symbols | HGNC |
| Â | Interaction | 913285 | miRNA-target interactions | mirTarBase,miRanda |
Relations | ANNOTATES | 514528 | Links to annotated entities | Gene ontology |
| Â | CONTAINS | 99979 | Links to entities in pathways | Reactome |
| Â | PRECURSOR_OF | 38558 | Precursors-matures relations | miRBase |
| Â | HAS_SNP | 236 | miRNAs-mutations relations | miRNASNP |
| Â | SYNONYM_OF | 115027 | Symbols-genes relations | HGNC |
| Â | REFERS_TO | 219132 | Accessions-proteins relations | UniProtKB |
| Â | INTERACTING_GENE | 913285 | Genes-interactions relations | mirTarBase,miRanda,miRNASNP |
| Â | INTERACTING_MIRNA | 657904 | miRNA-interactions relations | mirTarBase,miRanda |
| Â | INTERACTING_SNP | 255381 | SNPs-interactions relations | miRNASNP |