This document outlines the major changes to the EpiGraphDB platform and research. Please reach out to us for issues, feedbacks, suggestions and collaborations!
Graph database and platform v1.0
- Overhaul on the data integration pipeline and rebuild of the graph database.
- Major updates on the following sources:
- New integrated data sources
- Annotation of EBI GWAS traits to EFO
For specific details please refer to the version 1 changelog.
We have submitted EpiGraphDB R package to CRAN.
You can now
install.packages("epigraphdb") in R to get a stable version of the
We have submitted the preprint manuscript describing the EpiGraphDB platform to bioRxiv.
EpiGraphDB platform is now v0.3.0!
Graph database (API, and R package have been adapted the corresponding changes):
- Gtex node now called Tissue
- SNP node now called Variant
- Disease data now supplied by Mondo (https://mondo.monarchinitiative.org/)
- Literature nodes expanded and have extra properties from SemMedDB - backwards compatible as v0.2 pubmed_id property still exists
- SemMedDB data - SemmedTriple, SemmedTerm nodes
- MELODI literature enrichments
- Gwas-EFO via NLP
- Polygenic Risk Scores
- Ben Neale genetic correlation data
- EKDRD data
- MeSH data
- Old EFO relationships
- In house genetic correlation data (top SNPs)
The web UI (https://epigraphdb.org) has been refactored with a fresh new look.
- EpiGraphDB explorer https://epigraphdb.org/explore/
- EpiGraphDB gallery https://epigraphdb.org/gallery/
- v0.2 beta release for web application, API, and R package
- Pilot version