RNA-KG views

Here, we provide RNA-KG views generated by our team. Their specification 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 predictions tasks. For each view we also provide the correspondent meta-graph (in pdf and xlsx formats) and 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 that belong to the test sets.
• View 1: It includes triples involving miRNAs, genes, and diseases. During the construction of this view, the RNAdisease source was NOT included. The triples from this source are used as the test set. The goal is to assign a confidence value to miRNA-disease triples.
• View 4: It includes triples involving miRNAs, genes, and diseases. During the construction of this view, 10% of the miRNA-causes-disease triples were NOT included. These excluded triples are used as the test set. The goal is to assign a confidence value to the miRNA-disease triples and compare results with VIEW1.
• View 11: This complex view is designed for a heterogeneous link prediction task on edges of types miRNA-GO, lncRNA-GO, protein-GO, circRNA-GO, and lncRNA-disease.
• View 14: This view is designed for a (directional) link prediction task on edges of type piRNA←→disease/phenotype. The test set includes 10% of the triples from RNA-KG.
• View 15: This view is designed for a link prediction task on edges of type piRNA→disease. The test set includes triples from the piRBase source.