Schema analysis and shape extraction #2
Description
Identify which schema extractor to use at the start of the workflow.
Identified strengths and limitations:
| VoID generator | RDF-config | sheXer | |
|---|---|---|---|
| Overview of the tool | Extracts statistics from an RDF endpoint or a file | Automates SPARQL and schema diagram generation | Extracts ShEx and SHACL structure from an RDF graph |
| Documentation | Incomplete | Present | Present |
| Minimal requirement | Requires an RDF file or SPARQL endpoint; Graph must have triples with rdf:type predicates |
Requires manually curated model.yaml and prefix.yaml files |
Requires a Turtle file or a SPARQL endpoint |
| Data model representation | Object class-based file detailing all classes and properties | A set of tree structures representing classes and properties in YAML which can be exported as SVG | A SHACL or ShEx schema, optionally a UML diagram in PNG representing the shape graph |
| Process | Automated | Semi-automated | Automated, and optionally one can change the threshold used to accept patterns in the graph as shapes and I/O settings |
| Interpretability | Difficult; requires programming knowledge to understand organization of classes and properties | Easy; human-readable terms and graphical representation make the graph structure easily understandable | Easy; graphical representation facilitates quick interpretation |
| Readability | Human-readable terms (mapping ontology to labels); more compatible with programming language formats | Human-readable terms assigned for classes and properties | The diagrams and graphs are rendered with their URIs and no labels |
| Error reporting | Through Git issues | Through Git issues | Through Git issues |
| Implementation | Java (Native binary) | Ruby | Python |
| Limitation | Quadratic runtime for generating files (e.g., IDSM, OrthoDB); Not applicable for shape subclasses (e.g., In Rhea, where compounds are sub-classified into products, reactants, etc.) | Requires manual curation of input (Potential solution: integrate with VoID generators for semi-automation, for which a prototype exists) | The current algorithm is unable to detect specific patterns within the data; however, the developers are aware of this limitation. |