GenCoNet
Under development
Pipeline
- Prerequisites
- Most data downloads are automatic. However some databases like DrugBank need to be downloaded manually due to licensing or the need to register an account
- Download DrugBank full release to
data/DrugBank/drugbank_all_full_database.xml.zip
- Execute the DrugCentral queries and save them to the respective files
- Download OMIM
genemap2.txt
todata/OMIM/genemap2.txt
- Download DrugBank full release to
- Configure
data/config.json
to your Neo4j installation (bin path including admin tools)
- Most data downloads are automatic. However some databases like DrugBank need to be downloaded manually due to licensing or the need to register an account
- Execution
- Pre-processing
- Run
mondo.py
- Run
drugbank.py
- Run
drugcentral.py
- Run
disgenet.py
- Run
gwas_catalog.py
- Run
hgnc.py
- Run
hpo.py
(WIP) - Run
med_rt.py
- Run
ndf_rt.py
- Run
omim.py
- Run
superdrug2.py
- Run
pubmed.py
- Run
uniprotkb.py
- Run
gene_ontology.py
- Run
- Fusion
- Run
fusion.py
- Run
- Import database into Neo4j or directly use
[output-path]/graph.json
- Pre-processing