Schema analysis and shape extraction

Identify which schema extractor to use at the start of the workflow.
Identified strengths and limitations:

| | [VoID generator](https://github.com/JervenBolleman/void-generator) | [RDF-config](https://github.com/dbcls/rdf-config) | [sheXer](https://github.com/DaniFdezAlvarez/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](https://github.com/JervenBolleman/void-generator/blob/main/Tutorial.md) | [Present](https://github.com/dbcls/rdf-config/tree/master/doc) | [Present](https://github.com/DaniFdezAlvarez/shexer/blob/master/README.md) |
| **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](https://idsm.elixir-czech.cz/), [OrthoDB](https://www.orthodb.org/)); Not applicable for shape subclasses (e.g., In [Rhea](https://www.rhea-db.org/), 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. |