The OREGANO knowledge graph for computational drug repurposing

The files here are data files from the OREGANO project, which consists of building a holistic knowledge graph on drugs, including natural compounds. Here is the list of files:

- OREGANO_V2.tsv : The triplet file used for link prediction. 3 columns : Subjet ; Predicate ; Object

- oreganov2.1_metadata_complet.ttl : The OREGANO knowledge graph in turtle format with the names and cross-references of the various integrated entities.

The following files contain the cross-references of OREGANO entities according to their type. They are all organised as follows: the external sources are the titles of the columns and each line begins with the identifier of the entity in OREGANO :

- TARGET.tsv: Cross-reference table of the 22,096 targets.
- PHENOTYPES.tsv: Cross-reference table of the 11,605 phenotypes.
- DISEASES.tsv:  Cross-reference table of the 18,333 diseases.
- PATHWAYS.tsv: Cross-reference table of the 2,129 pathways.
- GENES.tsv: Cross-reference table of the 35,794 genes.
- COMPOUND.tsv:  Cross-reference table of the 90,868 compounds.
- INDICATIONS.tsv: Cross-reference table of the 2,714 indications.
- SIDE_EFFECT.tsv: Cross-reference table of the 6,060 side-effects.
- ACTIVITY.tsv: Names of the 78 activities.
- EFFECT.tsv: Names of the 171 effects.

The OREGANO knowledge graph is composed of 11 types of nodes and 19 types of links. The current version of the graph contains 88,937 nodes and 824,231 links.

A SPARQL endpoint has been provided to enable users to retrieve and explore the knowledge graph at OREGANO SPARQL endpoint .

The integration files and the knowledge graph are available on the GitHub of the OREGANO project in the Integration folder: Gitub repository .