Table 2

Most important edge types in Biomine
Edge type Source databases Count
Protein is associated to Protein STRING 2,916,000
Article refers to Node Entrez Gene, UniProt, KEGG, OMIM 2,250,000
Node has annotation GO Entrez Gene, UniProt, InterPro 1,365,000
Protein contains Feature UniProt 507,000
Gene is homologous to Gene HomoloGene 259,000
Gene codes for Protein Entrez Gene, STRING 174,000
Gene is located in Locus Entrez Gene, OMIM 151,000
Protein belongs to Family UniProt 114,000
Protein interacts with Protein Entrez Gene, UniProt 98,000
OMIM refers to OMIM OMIM 85,000
Gene participates in Pathway KEGG 65,000
GO has parent GO GO 56,000
InterPro has parent InterPro InterPro 20,000
Compound participates in Pathway KEGG 9,700
Gene affects Phenotype Entrez Gene 5,100
Phenotype is mapped to Locus OMIM 3,400
total 8,078,000

“Node” denotes any type of node, “OMIM” denotes nodes of type “Gene”, “Gene variant” or “Phenotype”, “GO” denotes nodes of type “Molecular function”, “Cellular component” or “Biological process“, and “InterPro” denotes nodes of type “Protein family” or “Protein feature”. Edge types with less than 3,000 instances are not listed.

Eronen and Toivonen

Eronen and Toivonen BMC Bioinformatics 2012 13:119   doi:10.1186/1471-2105-13-119

Open Data