Lymphoma KB

Setting up knowledge base

1. Install OrientDB and run from Docker Desktop
2. Run graph.py to initialize and populate graph knowledge base with variants and statements
3. To access the database, go to http://localhost:2480/ and login to lymphomakb database with username root and password root

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