RNA-KG views

Here, we provide RNA-KG views generated by our team. Their specifications are reported in a README.txt file. These views are thought to be used in combination with graph-oriented ML techniques for edge and node type labeling and heterogeneous/homogeneous link prediction tasks. For each view, the corresponding meta-graph (in pdf and xlsx formats) is provided along with two pickle dictionaries files for nodes and edges to facilitate the import in the GRAPE environment.

• View test: This view of test does not have 'semantic' value and should NOT be used as reliable or as a reference for predictions. The goal is to assign a confidence value to miRNA-disease and gene-miRNA triples.
• View miRNAdisease: It includes triples involving miRNAs, genes, and diseases. The goal is to assign a confidence value to miRNA-disease triples.
• View miRNAdiseaseSO: It includes triples involving miRNAs, genes, and diseases. Moreover, Sequence Ontology edges are integrated in the view. The goal is to assign a confidence value to the miRNA-disease triples and compare results with the miRNAdisease view.
• View RNAdiseaseGO: This complex view is designed for a heterogeneous link prediction task on edges of type miRNA-GO, lncRNA-GO, protein-GO, circRNA-GO, and lncRNA-disease.
• View piRNAdiseaseGO: This view is designed for a (directional) link prediction task on edges of type piRNA←→disease/phenotype.
• View lncRNAtRF: This view is designed for a link prediction task on edges of type lncRNA-anatomy, tRF-anatomy, lncRNA-cell, tRF-anatomy.