BMC Medical Informatics and Decision Making

Table 3 Overview of databases integrated in our current implementation of the data model indicating which type of data is provided (’+’) by each database

From: Variant information systems for precision oncology

	COSMIC	ClinVar	CIViC	Ensembl	1000 genomes	OncoKB	DrugBank	ClinicalTrials.gov	DGIdb	Cancer gene census	reactome	ncbi	DoCM	ExAC	canSAR	TCGA	GeneView	KEGG
Genome version	+	+		+	+					+			+		∼	+
Gene	+	+	+	+	+	+	∼	∼	+	+	+	+	+	+	+	+
Chromosome	+	+	+	+	+					+			+	+	∼	+
DNA position	+	+	+	+	+					+			+	+	∼	+
RefSeq transcript			+	+		+						+			∼	+
RefSeq protein		∼	+	+		+						+			∼	+
Somatic classification	∼	+		+	+			∼		+					+	+
DNA sub & position	+	+	+	+	+	∼							+	∼	∼	+
Protein sub & position	+	+	+	+	+	+							+	∼	∼	+
Variant type	+	+	+	+	+	+				+			+	+	+	+
Variant consequence	+	+	+	+		+				+				+	+	+
PMIDs	+	+	+			+	∼		+				+			∼	+	+
Cancer type	∼	+	+	+		∼		∼		+			+		+	+		+
Biomarker class			+			∼										+
Therapeutic context			+	+		∼	∼	∼	+							+
Effect			+	+			∼	∼								+
Level of evidence	+		+	+		∼				+
Sublevel of evidence			+			∼
Pathway							∼	∼			+				+			+
Drug			+				+	∼	+
Clinical significance			+				+
Molecular mechanism							+
Fully integrated	+	+	+	+	+	+	+	+	+	+	+	+	+	+
Specifically linked															+	+	+	+

In some cases the information is provided only in part (’ ∼’), meaning that either references to other sources are provided which hold the needed information or that the information is provided only for a subset of entities

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