GenomicKB

Genomic Knowledgebase (GenomicKB) is a database that uses a knowledge graph to consolidate genomic datasets and annotations. GenomicKB integrates data from more than 30 consortia, in which the genomic entities and relationships are represented as diverse nodes and edges with properties.

Learn more from the original GenomicKB article >>
The brief concept graph of gkb

Cite: Feng, Fan, et al. "GenomicKB: a knowledge graph for the human genome." Nucleic Acids Research 51.D1 (2023): D950-D956. https://doi.org/10.1093/nar/gkac957

318,790,570
Nodes

1,131,257,092
Edges

3,902,460,300
Attributes

Example 1

Let's start with an easy question:

which common genomic variants locate in a gene of interest?
sample 1 picture

Example 2

Use eQTLs to match enhancers with genes!

Gene-enhancer pairs are identified when one eQTL locates in an enhancer and correlate with the expression of a nearby gene.

sample 2 picture

Example 3

Find "structural" loops in K562!

Loops are strong 3D interactions between genomic regions, which might be correlated with CTCF binding and/or transcriptional regulation. We define "structural" loops as loops whose anchors are bound by CTCF.
sample 3 picture

Example 4

Let's validate whether GWAS SNPs of type II diabetes locate in genes that are activated in pancreas!
sample 4 picture