EpiGraphDB graph database

The EpiGraphDB database is built using neo4j, a graph database technology:

Below is a simple representation of EpiGraphDB as a meta graph (http://epigraphdb.org/about):

And below is the schema of the graph database (http://api.epigraphdb.org/meta/schema?graphviz=true&plot=true):

Data sources

EpiGraphDB integrates data generated at the MRC IEU with data from a range of third party sources. These include¹:

• UK Biobank genome-wide association study results from the IEU GWAS database: https://gwas.mrcieu.ac.uk
• MR-EvE causal estimates: https://doi.org/10.1101/173682
• Reactome pathway data: https://reactome.org/
• STRING protein association data: https://string-db.org/
• IntAct molecular interaction data: https://www.ebi.ac.uk/intact/
• Semantic predications from SemMedDB: https://skr3.nlm.nih.gov/SemMedDB/
• Experimental factor ontology (EFO) terms: https://www.ebi.ac.uk/efo/
• Drug-target relationships from Open Targets: https://www.targetvalidation.org/
• Gene-drug relationships from Clinical Pharmacogenetics Implementation Consortium (CPIC): https://cpicpgx.org/genes-drugs/
• Gene and Protein data from BioMart Ensembl: http://www.ensembl.org/biomart
• Tissue specific gene expression data from GTEx: https://gtexportal.org/home/
• Disease data from Mondo Disease Ontology: https://mondo.monarchinitiative.org/
• Druggable genes: https://stm.sciencemag.org/content/suppl/2017/03/27/9.383.eaag1166.DC1
• Expression quantitative trait locus (eQTL) data from the eQTLGen consortium: https://www.eqtlgen.org/
• Protein quantitative trait locus (pQTL) data from plasma proteins: http://epigraphdb.org/risk-factor-drugs/
• GWAS to UMLS relationships: https://metamap.nlm.nih.gov/MetaMapLite.shtml
• Polygenic Risk Score from PRS Atlas http://mrcieu.mrsoftware.org/PRS_atlas/
• Genetic correlation data from Neale Lab https://ukbb-rg.hail.is/
• Observational correlation data from UK Biobank https://www.ukbiobank.ac.uk/
• xQTL study project Zheng et al., forthcoming
• Vectology http://vectology.mrcieu.ac.uk
• Monarch Initiative https://monarchinitiative.org/

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1. For the full list of source data and how they are integrated into EpiGraphDB please refer to our documentation on meta nodes and meta relationships. ↩