- Install OrientDB and run from Docker Desktop
- Run
graph.py
to initialize and populate graph knowledge base with variants and statements - To access the database, go to http://localhost:2480/ and login to
lymphomakb
database with usernameroot
and passwordroot
Currently incorporated sources:
- NCIt: https://evs.nci.nih.gov/ftp1/NCI_Thesaurus/Thesaurus.FLAT.zip
- ClinVar: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/tab_delimited/variant_summary.txt.gz
Currently supported variant types:
- Single nucleotide variant
- Copy gain/loss
- Indel
- Insertion
- Deletion
No. of diseases: 889
No. of variants: 201
No. of statements: 399