Alternative to PrimeKG · OWL Ontology-based
BioKGKnowledge Graph
Heterogeneous biomedical knowledge graph constructed from 8 OWL ontologies using SPARQL triple extraction and cross-ontology alignment.
HGNC · OGG · MONDO · NBO · HENEGEO · NPO · NIGO · AIO
◉
35
Total Nodes
across 8 node types
⟷
38
Total Edges
17 relation types
📂
8
OWL Sources
ontology files parsed
◈
24
Attributes
unique node properties
3. Node Types (8)
🧬
Gene8 nodes
🦠
Disease6 nodes
💊
Drug5 nodes
🧠
Behavior6 nodes
⚡
Neuron4 nodes
🫁
Anatomy2 nodes
🔗
Pathway2 nodes
🔬
Phenotype2 nodes
5. Relationships (17)
associated_with6
driver_mutation2
expressed_in1
causes1
targets2
modulates2
inhibits2
treats5
participates_in2
activates2
regulates2
mediated_by2
regulated_by1
has_phenotype2
is_site_of2
dysregulated_in3
interacts_with1
1. Alternative Development Method
📂
STEP 01
OWL Parsing
Parse RDF/OWL XML with ElementTree or rdflib. Extract owl:Class, rdfs:label, owl:ObjectProperty, rdfs:subClassOf triples.
⛏
STEP 02
Triple Extraction
Execute SPARQL SELECT queries to pull (Subject, Predicate, Object) triples. Normalize IRIs across ontologies via shared cross-references.
🔗
STEP 03
Cross-Ontology Align
Match HGNC↔OGG via HGNC IDs. Align MONDO↔HENEGEO via disease xrefs. Link NPO↔NBO via behavior-neuron co-occurrence.
🕸
STEP 04
Graph Build
Construct heterogeneous typed graph. Store as JSON nodes+edges. Validate completeness, connectivity, and consistency.
2. Data Repositories (8 OWL Files)
HGNC
hgnc.owlStandardized human gene symbols and names
8
nodes
OGG
ogg-merged.owlBiological ontology for genes and genomes
8
nodes
MONDO
mondo-simple.owlUnified cross-species disease ontology
6
nodes
NBO
nbo.owlHuman and animal behavioral ontology
6
nodes
HENEGEO
HENEGEO_v1_0.owlCancer treatment and clinical ontology
5
nodes
NPO
npo.ttlNeuron type classification ontology
6
nodes
NIGO
NIGO_vv1.owlGene-imaging-neurological links
2
nodes
AIO
aio-full.owlDeep learning networks and AI models
0
nodes