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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                + + + +
  1. 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