iBKH integrates data from 17 publicly available biomedical databases. The current version of iBKH contains a total of 2,384,501 entities of 11 types. Specifically, the iBKH includes 23,003 anatomy entities, 19,236 disease entities, 37,997 drug entities, 88,376 gene entities, 2,065,015 molecule entities, 1,361 symptom entities, 4,101 DSI entities, 137,568 DSP entities, 605 TC entities, 2,988 pathway entities and 4,251 side-effect entities. For the relationships in the iBKH, there are 86 relation types within 18 kinds of entity pairs, including Anatomy-Gene, Drug-Disease, Drug-Drug, Drug-Gene, Disease-Disease, Disease-Gene, Disease-Symptom, Gene-Gene, DSI-Disease, DSI-Symptom, DSI-Drug, DSI-Anatomy, DSI-DSP, DSI-TC, Disease-Pathway, Drug-Pathway, Gene-Pathway and Drug-Side Effect. In total, iBKH contains 48,194,646 relations.
Our ultimate goal was to build a biomedical knowledge graph via comprehensively incorporating biomedical knowledge as much as possible. To this end, we collected and integrated 17 publicly available data sources to curate a comprehensive one. Details of the used data resources were listed in Table.
| Entity Type | Number | Included Identifiers |
|---|---|---|
| Anatomy | 23,003 | Uberon ID, BTO ID, MeSH ID, Cell Ontology ID |
| Disease | 19,236 | Disease Ontology ID, PharmGKB ID, MeSH ID, OMIM ID |
| Drug | 37,997 | DrugBank 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, Gene Ontology ID |
| Side-Effect | 4,251 | UMLS CUI |
| Total Entities | 2,384,501 | - |
| Relation Type | Number |
|---|---|
| Anatomy-Gene | 12,171,021 |
| Drug-Disease | 2,717,947 |
| Drug-Drug | 2,684,682 |
| Drug-Gene | 1,303,747 |
| Disease-Disease | 11,072 |
| Disease-Gene | 27,538,774 |
| Disease-Symptom | 3,357 |
| Gene-Gene | 735,156 |
| DSI-Symptom | 2,093 |
| DSI-Disease | 5,134 |
| DSI-Drug | 3,057 |
| DSI-Anatomy | 4,334 |
| DSP-DSI | 689,297 |
| DSI-TC | 5,430 |
| Disease-Pathway | 1,941 |
| Drug-Pathway | 3,231 |
| Gene-Pathway | 152,243 |
| Drug-Side Effect | 163,206 |
| Total Relations | 48,194,646 |
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.
@article{su2021ibkh,
title={iBKH: The integrative Biomedical Knowledge Hub},
author={Su, Chang and Hou, Yu and Guo, Winston and Chaudhry, Fayzan and Ghahramani, Gregory and Zhang, Haotan and Wang, Fei},
journal={medRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory Press}，
url = {https://www.medrxiv.org/content/10.1101/2021.03.12.21253461v3}
}