CRC Organoid Knowledge Graph

This deposit contains a knowledge graph for a patient-derived colorectal cancer (CRC) organoid cohort: the RDF schema and controlled vocabularies, the declarative table-to-RDF mappings, the SHACL validation shapes, the build, validation, and reasoning pipeline, and a synthetic example cohort that exercises the whole pipeline. It models the cohort's metadata, such as the patients, biospecimens, the tumor/normal status of each specimen, their derivation relationships, and which assays exist per specimen, as a scaffold that joins to a larger multi-omics graph through shared biospecimen identifiers. An upper-level ontology alignment to the Semanticscience Integrated Ontology (SIO), and first-class provenance (PROV-O) for derivation, exclusions, and conflicting records. Validation is structural (SHACL / pySHACL), logical (merged with SIO and classified with ELK, cross-checked with HermiT via ROBOT), and functional (competency questions federated against external ontology authorities). No patient data is included. The deposit contains only code, schema, documentation, and a synthetic fixture cohort. The real cohort's materialized RDF, crosswalk tables, and clinical inputs are withheld in accordance with research ethics governance. To run the pipeline, supply inputs in the documented format; all documents and data are also available in the repository at https://github.com/bio-ontology-research-group/CRC_KG.git.