MitoKG: A Pretrained Mitochondrial Heterogeneous Knowledge Graph

MitoKG is a mitochondrial-focused heterogeneous knowledge graph. It extracts only the mitochondria-relevant subset of five public biomedical databases (MitoCarta 3.0, STRING v12.0, Reactome, DrugBank, and CORUM 5.2). Starting from the MitoCarta 3.0 human core mitochondrial gene list, 984 unique gene symbols are retained; these map to 1,132 canonical UniProt entries, which form the gene/protein nodes of the graph. Only edges and auxiliary nodes connected to this core set are kept. Graph composition:- 4 node types: gene/protein (1,132 UniProt entries, corresponding to 984 MitoCarta core gene symbols), pathway (815), drug (305), protein complex (297). Total nodes: 2,549.- 5 forward edge types: protein-protein interaction from STRING at high confidence (14,763 edges), gene-pathway membership from Reactome (5,990 edges), drug-target from DrugBank (656 edges), gene-complex membership from CORUM (806 edges), and pathway hierarchy from Reactome (804 edges). Total forward edges: 23,019.- Coverage over the 984 core mitochondrial genes: 970 with at least one PPI, 860 with at least one pathway, 345 with at least one complex membership, and 292 with at least one drug targeting. A Heterogeneous Graph Transformer (HGT) was pretrained on this graph, producing 64-dimensional node embeddings that can be used directly as mitochondria-aware gene features in downstream models. Released artifacts: the HeteroData graph object, HGT model weights, 64-dim embeddings for the 984 unique gene symbols (gene_embeddings.npy), 64-dim embeddings for all 1,132 UniProt entries in the graph (all_gene_embeddings.npy), a UniProt ID whitelist of the 1,132 entries, and node-index mappings. Source databases retain their original licences; MitoKG does not redistribute raw tables from MitoCarta, STRING, Reactome, DrugBank, or CORUM.MitoKG是一款聚焦线粒体的异质知识图谱（heterogeneous knowledge graph）。它仅从五个公开生物医学数据库（MitoCarta 3.0、STRING v12.0、Reactome、DrugBank及CORUM 5.2）中提取与线粒体相关的子集。以MitoCarta 3.0的人类核心线粒体基因列表为起点，共保留984个独特基因符号，这些符号映射至1132条标准通用蛋白数据库（Universal Protein Resource，简称UniProt）条目，构成该图谱的基因/蛋白质节点。仅保留与该核心集合相连的边与辅助节点。 图谱组成如下： - 共4类节点：基因/蛋白质（1132条UniProt条目，对应984个MitoCarta核心基因符号）、通路（815个）、药物（305个）、蛋白质复合物（297个），总节点数为2549个。 - 共5种正向边类型：来自STRING的高置信度蛋白质-蛋白质相互作用边（14763条）、来自Reactome的基因-通路归属边（5990条）、来自DrugBank的药物-靶点边（656条）、来自CORUM的基因-复合物归属边（806条），以及来自Reactome的通路层级边（804条），正向边总数量为23019条。 - 针对984个核心线粒体基因的覆盖情况：970个基因至少拥有1条蛋白质相互作用边，860个基因至少归属1条通路，345个基因至少具备1个复合物归属关系，292个基因至少存在1种靶向药物。 研究团队基于该图谱预训练了异构图Transformer（Heterogeneous Graph Transformer，简称HGT），生成了64维的节点嵌入，可直接作为线粒体感知的基因特征应用于下游模型。 本次发布的成果包括：HeteroData图谱对象、HGT模型权重、针对984个独特基因符号的64维嵌入（gene_embeddings.npy）、针对图谱中全部1132条UniProt条目的64维嵌入（all_gene_embeddings.npy）、1132个条目的UniProt ID白名单，以及节点索引映射表。 原始来源数据库保留其原有许可协议；MitoKG不会重新分发来自MitoCarta、STRING、Reactome、DrugBank或CORUM的原始数据表。