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:<br>- 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.<br>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.<br>- PHENOTYPES.tsv: Cross-reference table of the 11,605 phenotypes.<br>- DISEASES.tsv: Cross-reference table of the 18,333 diseases.<br>- PATHWAYS.tsv: Cross-reference table of the 2,129 pathways.<br>- GENES.tsv: Cross-reference table of the 35,794 genes.<br>- COMPOUND.tsv: Cross-reference table of the 90,868 compounds.<br>- INDICATIONS.tsv: Cross-reference table of the 2,714 indications.<br>- SIDE_EFFECT.tsv: Cross-reference table of the 6,060 side-effects.<br>- ACTIVITY.tsv: Names of the 78 activities.<br>- 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 .<br>The integration files and the knowledge graph are available on the GitHub of the OREGANO project in the Integration folder: Gitub repository .

本仓库内的文件均源自OREGANO项目的数据文件，该项目旨在构建涵盖药物（含天然化合物）的一体化知识图谱（knowledge graph）。以下为文件清单：
- OREGANO_V2.tsv：用于链接预测的三元组文件，共包含3列：主体（Subject）、谓词（Predicate）、客体（Object）。
- oreganov2.1_metadata_complet.ttl：采用Turtle格式（Turtle）存储的OREGANO知识图谱文件，内含各集成实体的名称与交叉引用信息。

下述文件按实体类型整理了OREGANO实体的交叉引用表，其组织结构统一为：列标题即为各外部数据源，每行均以OREGANO内部的实体标识符作为起始：
- TARGET.tsv：收录22096个靶点的交叉引用表
- PHENOTYPES.tsv：收录11605种表型的交叉引用表
- DISEASES.tsv：收录18333种疾病的交叉引用表
- PATHWAYS.tsv：收录2129条通路的交叉引用表
- GENES.tsv：收录35794个基因的交叉引用表
- COMPOUND.tsv：收录90868种化合物的交叉引用表
- INDICATIONS.tsv：收录2714项适应症的交叉引用表
- SIDE_EFFECT.tsv：收录6060种不良反应的交叉引用表
- ACTIVITY.tsv：收录78项活性名称
- EFFECT.tsv：收录171项效应名称

OREGANO知识图谱共包含11类节点与19类关联边。当前版本的图谱包含88937个节点与824231条关联边。

项目已提供SPARQL端点（SPARQL endpoint），供用户检索并探索该知识图谱，访问入口为OREGANO SPARQL endpoint。

本项目的集成文件与知识图谱已上传至OREGANO项目的GitHub仓库（GitHub repository）的Integration文件夹中，具体地址为Gitub repository。