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 .

本仓库收录的文件均源自OREGANO项目的数据文件，该项目旨在构建一套覆盖药物（含天然化合物）的全域知识图谱。以下为文件清单：<br>- OREGANO_V2.tsv：用于链路预测的三元组文件，共包含3列，分别为主体、谓词、客体。<br>- oreganov2.1_metadata_complet.ttl：采用Turtle格式存储的OREGANO知识图谱文件，内含各类已整合实体的名称与交叉引用信息。<br>以下文件按实体类型分类，提供OREGANO实体的交叉引用信息，所有文件均遵循统一格式：列标题对应外部数据源名称，每行以OREGANO内部实体标识符作为起始字段：<br>- TARGET.tsv：收录22096个靶点的交叉引用表<br>- PHENOTYPES.tsv：收录11605种表型的交叉引用表<br>- DISEASES.tsv：收录18333种疾病的交叉引用表<br>- PATHWAYS.tsv：收录2129条通路的交叉引用表<br>- GENES.tsv：收录35794个基因的交叉引用表<br>- COMPOUND.tsv：收录90868种化合物的交叉引用表<br>- INDICATIONS.tsv：收录2714项适应症的交叉引用表<br>- SIDE_EFFECT.tsv：收录6060种不良反应的交叉引用表<br>- ACTIVITY.tsv：收录78项活性的名称列表<br>- EFFECT.tsv：收录171种效应的名称列表<br>OREGANO知识图谱共包含11种节点类型与19种边类型，当前版本的图谱包含88937个节点与824231条边。<br>项目已提供SPARQL查询端点（SPARQL endpoint），供用户检索与探索该知识图谱，访问入口为OREGANO SPARQL endpoint。<br>该项目的整合文件与知识图谱已上传至OREGANO项目GitHub仓库的Integration文件夹中，仓库地址为Gitub repository。