REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
Bgee	Bastian et al., 202131	https://bgee.org/
Brenda Tissue Ontology	Chang et al., 202127	https://www.brenda-enzymes.org/index.php
Cell Ontology	Diehl et al., 201628	http://obofoundry.org/ontology/cl.html
Comparative Toxicogenomics Database (CTD)	Davis et al., 201932	http://ctdbase.org/
ChEMBL	Gaulton et al., 201242	https://www.ebi.ac.uk/chembl/
Chemical Entities of Biological Interest (ChEBI)	de Matos et al., 201043	https://www.ebi.ac.uk/chebi/init.do
Drug Repurposing Knowledge Graph (DRKG)	Ioannidis et al., 202039	https://github.com/gnn4dr/DRKG
Disease Ontology	Schriml et al., 201229	https://disease-ontology.org/
DrugBank	Wishart et al., 201833	https://go.drugbank.com/
Hetionet	Himmelstein et al., 20174	https://github.com/hetio/hetionet
HUGO Gene Nomenclature Committee (HGNC)	Braschi et al., 201941	https://www.genenames.org/
Integrated Dietary Supplement Knowledge Base (iDISK)	Rizvi et al., 202040	https://conservancy.umn.edu/handle/11299/204783
Kyoto Encyclopedia of Genes and Genomes (KEGG)	Kanehisa and Goto, 200034	https://www.kegg.jp/
Pharmacogenetics Knowledge Base (PharmGKB)	Hewett et al., 200235	https://www.pharmgkb.org/
Reactome	Fabregat et al., 201836	https://reactome.org/
Side effect resource (SIDER)	Kuhn et al., 2016	http://sideeffects.embl.de/
TISSUE	Palasca et al., 201838	https://tissues.jensenlab.org/
Uberon	Mungall et al., 201230	https://www.ebi.ac.uk/ols/ontologies/uberon
Unified Medical Language System (UMLS)	Bodenreider, 200487	https://www.nlm.nih.gov/research/umls/index.html
iBKH source files	This paper	https://github.com/wcm-wanglab/iBKH/tree/main/iBKH
iBKH portal	This paper	http://ibkh.ai/
Software and algorithms
Neo4j	Neo4j, Inc.	https://neo4j.com
Python	Python Software Foundation	https://www.python.org
Django	Django Software Foundation	https://www.djangoproject.com
neovis.js	Neo4j Contrib	https://github.com/neo4j-contrib/neovis.js
D3.js	Mike Bostock	https://d3js.org
DGL-KE (Deep Graph Library – Knowledge Graph Embedding)	Zheng et al., 202026	https://github.com/awslabs/dgl-ke
iBKH construction and iBKH-based knowledge discovery	This paper	https://github.com/wcm-wanglab/iBKH