barryrun / ibkh

iBKH: The integrative Biomedical Knowledge Hub

integrative Biomedical Knowledge Hub (iBKH)

iBKH integrates data from 18 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.

Materials and Methods

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 18 publicly available data sources to curate a comprehensive one. Details of the used data resources were listed in Table.

Statistics of iBKH

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 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

Licence

The data of iBKH is licensed under the MIT License. The iBKH integrated the data from many resources, and users should consider the licenses for each of them (see the detail in the table).

Cite

@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}
}