About Us

Biomedicine is a discipline with enormous volume of highly specialized biomedical knowledge accumulated from biological experiments and healthcare practices.

The emerging biomedical knowledge graph (BKG) has become a novel paradigm for better management of the massive volume, sophisticated biomedical knowledge and has attracted significant attention in recent years. A BKG is a graph that integrates, harmonizes, and stores biomedical knowledge from single or multiple expert-derived knowledge sources, where nodes are a set of biomedical entities (e.g., diseases, drugs, genes, biological processes, etc.) and edges between nodes (i.e., entities) are relations linking the biomedical entities.

iBKH (Integrative Biomedical Knowledge Hub) is a comprehensive biomedical knowledge graph. Current iBKH version 1.0 contains 2,384,501 entities of 11 types and 48,194,646 relations of 45 types of relations within 18 kinds of entity pairs.


  • Comprehensive: To date, iBKH has involved biomedical knowledge from 18 sources, including not only the biomedical ontologies and biomedical knowledge bases, but also existing BKGs that have integrated diverse sources.
  • A web-based, easy-to-use, publicly available graphical portal for fast, interactive, and visualized biomedical knowledge retrieval in iBKH.
  • An efficient and scalable graph learning module for novel knowledge discovery in iBKH.
iBKH Schema

Each circle denotes an entity type, and each link denotes a meta relation between a pair of entities. Of note, a meta relation can represent multiple types of relations between a specific pair of entities. For example, five potential relations including ‘Associates’, ‘Downregulates’, ‘Upregulates’, ‘Inferred_Relation’, ‘Text_Semantic_Relation’ can exist between a pair of disease and gene entities.

iBKH Statistics

Entity Statistics

Entity Type Number Included Identifiers
Anatomy 23,003 Uberon ID, BTO ID, MeSH ID, Cell Ontology ID
Disease 19,236 Disease Ontology ID, KEGG ID, PharmGKB ID, MeSH ID, OMIM ID
Drug 37,997 DrugBank ID, KEGG ID, PharmGKB ID, MeSH ID
Gene 88,376 HGNC ID, NCBI ID, PharmGKB ID
Molecule 2,065,015 CHEMBL ID, CHEBI ID
Symptom 1,361 MeSH ID
Dietary Supplement Ingredient 4,101 iDISK ID
Dietary Supplement Product 137,568 iDISK ID
Therapeutic Class 605 iDISK ID, UMLS CUI
Pathway 2,988 Reactome ID, KEGG ID, Gene Ontology ID
Side-Effect 4,251 UMLS CUI
Total Entities 2,384,501 -

Relation Statistics

Entity pair Total number of relations between the entity pairs Relation types Number of relations of the specific type
Anatomy-Gene 12,171,021 Anatomy-Express-Gene 10,388,168
Anatomy-Absent-Gene 2,837,741
Drug-Disease 2,717,947 Drug-Palliates-Disease 390
Drug-Treats-Disease 5,492
Drug-Effect-Disease 5,136
Drug-Associate-Disease 96,458
Drug-Inferred Relation-Disease 2,589,522
Drug-Text_Semantic-Disease 50,653
Drug-Drug 2,684,682 Drug-Interaction DrugBank-Drug 2,682,157
Drug-Resemble Hetionet-Drug 6,486
Drug-Gene 1,303,747 Drug-Target-Gene 16,518
Drug-Transporter-Gene 3,066
Drug-Enzyme-Gene 5,241
Drug-Carrier-Gene 853
Drug-Downregulates-Gene 66,994
Drug-Upregulates-Gene 72,361
Drug-Associate-Gene 19,434
Drug-Binds-Gene 11,571
Drug-Interaction-Gene 1,181,492
Drug-Text Semantic-Gene 68,429
Disease-Disease 11,072 Disease-is a-Disease 10,529
Disease-Resemble-Disease 543
Disease-Gene 27,538,774 Disease-Associate-Gene 47,965
Disease-Downregulates-Gene 7,623
Disease-Upregulates-Gene 7,731
Disease-Inferred Relation-Gene 27,454,631
Disease-Text Semantic-Gene 94,759
Disease-Symptom 3,357 Disease-Present-Symptom 3,357
Gene-Gene 735,156 Gene-Covaries-Gene 61,690
Gene-Interacts-Gene 147,164
Gene-Regulates-Gene 265,672
Gene-Associate-Gene 2,602
Gene-Text Semantic-Gene 301,752
DSI-Symptom 2,093 DSI-has adverse reaction-Symptom 2,093
DSI-Disease 5,134 DSI-is effective for-Disease 5,134
DSI-Drug 3,057 DSI-interacts-Drug 3,057
DSI-Anatomy 4,334 DSI-has adverse effect on-Anatomy 4,334
DSP-DSI 689,297 DSP-has ingredient-DSI 689,297
DSI-TC 5,430 DSI-has therapeutic class-TC 5,430
Gene-Pathway 152,243 Gene-Reaction-Pathway 118,480
Gene-Association-Pathway 47,742
Disease-Pathway 1,941 Disease-Association-Pathway 1,941
Drug-Pathway 3,231 Drug-Association-Pathway 3,231
Drug-Side effect 163,206 Drug-cause-Side effect 163,206
  • Sep. 2022 - iBKH User Interface add Cohort Context Exploration application!
  • Mar. 2022 - iBKH User Interface add Link Prediction application!
  • Nov. 2021 - iBKH User Interface add Search Module!
  • Jun. 2021 - iBKH User Interface created!
  • May. 2021 - iBKH add Anatomy and Dietary Supplements!
  • Apr. 2021 - iBKH created!

The data of iBKH is licensed under the CC BY-NC-SA 4.0. The iBKH integrated the data from many resources, and users should consider the licenses for each of them (see the detail in the table). For sources with defined licenses, we apply the license attribute on a per-node and per-edge basis. However, some sources do not provide any licenses, so for those, we have requested permission.


    title = {Biomedical Discovery through the integrative Biomedical Knowledge Hub (iBKH)},,
    author = {Su, Chang and Hou, Yu and Rajendran, Suraj and Maasch, Jacqueline R. M. A. and Abedi, Zehra and Zhang, Haotan and Bai, Zilong and Cuturrufo, Anthony and Guo, Winston and Chaudhry, Fayzan and Ghahramani,
                    Gregory and Tang, Jian and Cheng, Feixiong and Li, Yue and Zhang, Rui and Bian, Jiang and Wang, Fei},
    journal = {medRxiv},
    year = {2022},
    doi = {10.1101/2021.03.12.21253461},
    publisher = {Cold Spring Harbor Laboratory Press},
    URL = {},
    journal = {medRxiv}