Fig 1.
A construct query is type of SPARQL query that enables the conversion of one graph pattern to another.
Here an interaction described by its spatial properties (GPML) is converted into a semantic representation reflecting its biological interpretation (WP). The SPARQL query is available in the supporting information section.
Table 1.
Example queries handled by the WikiPathways SPARQL endpoint.
Table 2.
Example federated queries handled by the WikiPathways SPARQL endpoint.
Fig 2.
The colored boxes represent genes which are up (red) or down (blue) regulated in diabetes mellitus.
PIK3R2, MYO1C, PRKAA2, LIPE are down regulated in pre-diabetes. STX4A is down regulated in type 1 diabetes longstanding. PRKCQ, PTPN11, FOXO3A are down regulated in type 2 diabetes. GAB1, RHEB, MAP4K4, SNAP23 are up regulated in pre-diabetes. RHOJ, PRKCB are up regulated in type 1 diabetes recent onset. MAPK14UP, EIF4EBP1 are up regulated in type 1 diabetes clinical onset. From these 17 up or down regulated genes, 9 are being reported as being in the top 10 disease and phenotype associations for the selected gene in DisGeNET (i.e. PIK3R2, PRKAA2, LIPE, STX4A, PRKCQ, FOXO3A, MAP4K4, SNAP23, and PRKCB) (Gene-disease association data were retrieved from the DisGeNET Database, GRIB/IMIM/UPF Integrative Biomedical Informatics Group, Barcelona. (http://www.disgenet.org/). 04, 2016)