This reproducibility package contains the complete set of technical research artifacts, data models, schemas, and software components supporting the manuscript "Enabling Clinical Research with Semantic Knowledge Graphs: The Cancer Virtual Lab Platform". Package Contents: CVL-O Ontology: The core OWL2 domain ontology formalising the oncological care pathway (86 classes, >100 properties, integrating standard clinical terminologies). The navigable HTML documentation (English and Italian) and an interactive graph view are available online at Cancer-Virtual-Lab-Public-Repo/ontology. FHIR Implementation Guide: Complete HL7 FHIR R4 Implementation Guide including FSH source profiles, value sets, code systems, extensions, and the navigable HTML documentation build. Mapping rules: Declarative ETL transformation rules dictating how raw clinical structures are mapped into FHIR JSON resources. GraphDB rule sets: Custom Programmed Inference Engine (.pie) rule set configured for Ontotext GraphDB and used for OWL 2 RL clinical inference, along with the complementary SPARQL clinical reasoning rules for non-monotonic abstractions. Validation reports: Raw HAPI FHIR Validator OperationOutcome reports covering 31,070 clinical records across all 19 CVL profiles, providing the empirical evidence base for the manuscript. NL query component: Complete source code (LangGraph agent, multi-index ChromaDB RAG, FastAPI backend, Streamlit UI) and explicit prompt engineering catalogs for ontology-grounded Text-to-SPARQL translation.
De Angelis, P., Carbonaro, A., Andalò, A., Giorgetti, L., Di Donato, C., Pasolini, R., et al. (2026). Reproducibility package for: Enabling Clinical Research with Semantic Knowledge Graphs: The Cancer Virtual Lab Platform.
Reproducibility package for: Enabling Clinical Research with Semantic Knowledge Graphs: The Cancer Virtual Lab Platform
Carbonaro, Antonella;Andalò, Alice;Giorgetti, Luca;Di Donato, Cristian;Pasolini, Roberto;
2026
Abstract
This reproducibility package contains the complete set of technical research artifacts, data models, schemas, and software components supporting the manuscript "Enabling Clinical Research with Semantic Knowledge Graphs: The Cancer Virtual Lab Platform". Package Contents: CVL-O Ontology: The core OWL2 domain ontology formalising the oncological care pathway (86 classes, >100 properties, integrating standard clinical terminologies). The navigable HTML documentation (English and Italian) and an interactive graph view are available online at Cancer-Virtual-Lab-Public-Repo/ontology. FHIR Implementation Guide: Complete HL7 FHIR R4 Implementation Guide including FSH source profiles, value sets, code systems, extensions, and the navigable HTML documentation build. Mapping rules: Declarative ETL transformation rules dictating how raw clinical structures are mapped into FHIR JSON resources. GraphDB rule sets: Custom Programmed Inference Engine (.pie) rule set configured for Ontotext GraphDB and used for OWL 2 RL clinical inference, along with the complementary SPARQL clinical reasoning rules for non-monotonic abstractions. Validation reports: Raw HAPI FHIR Validator OperationOutcome reports covering 31,070 clinical records across all 19 CVL profiles, providing the empirical evidence base for the manuscript. NL query component: Complete source code (LangGraph agent, multi-index ChromaDB RAG, FastAPI backend, Streamlit UI) and explicit prompt engineering catalogs for ontology-grounded Text-to-SPARQL translation.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
