├── .claude ├── .mcp.json └── settings.json ├── .github ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── actions │ ├── claude-code-action │ │ └── action.yml │ ├── claude-issue-summarize-action │ │ └── action.yml │ └── claude-issue-triage-action │ │ └── action.yml ├── ai-controllers.json ├── copilot-instructions.md ├── copilot-setup-steps.yml └── workflows │ ├── claude-code-review.yml │ ├── claude-issue-summarize.yml │ ├── claude-issue-triage.yml │ ├── claude-ontology-review.yml │ ├── claude.yml │ ├── deploy_documentation.yml │ ├── dragon-ai.yml │ ├── main.yaml │ └── pypi-publish.yaml ├── .gitignore ├── .goosehints ├── AGENTS.md ├── CLAUDE.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── bin └── README.txt ├── conf └── obograph-style.json ├── config.env ├── db └── README.md ├── demo └── cam │ └── README.md ├── docgen-templates ├── class.md.jinja2 ├── common_metadata.md.jinja2 ├── enum.md.jinja2 ├── index.md.jinja2 ├── index.tex.jinja2 ├── schema.md.jinja2 ├── slot.md.jinja2 ├── subset.md.jinja2 └── type.md.jinja2 ├── indexes └── all-indexes.sql ├── install.Makefile ├── mkdocs.yml ├── notebooks └── SemanticSQL-Tutorial.ipynb ├── ontologies.Makefile ├── poetry.lock ├── pyproject.toml ├── reports └── obo.tsv ├── sparql └── skos-to-owl.ru ├── src └── semsql │ ├── __init__.py │ ├── builder │ ├── build.Makefile │ ├── builder.py │ ├── cli.py │ ├── exclude-terms.txt │ ├── indexes │ │ └── all-indexes.sql │ ├── prefixes │ │ ├── obo_prefixes.csv │ │ ├── obo_prefixes.db │ │ ├── obo_prefixes.owl │ │ ├── obo_prefixes.ttl │ │ ├── prefix.sql │ │ ├── prefix_ddl.sql │ │ ├── prefixes.csv │ │ ├── prefixes_curated.csv │ │ └── prefixes_local.csv │ ├── registry │ │ ├── __init__.py │ │ ├── ontologies.yaml │ │ ├── registry_schema.py │ │ └── registry_schema.yaml │ └── sql_schema │ │ ├── obo.sql │ │ ├── omo.sql │ │ ├── owl.sql │ │ ├── rdf.sql │ │ ├── relation_graph.sql │ │ └── semsql.sql │ ├── linkml │ ├── __init__.py │ ├── basics.yaml │ ├── chebi.yaml │ ├── nlp.yaml │ ├── obo.yaml │ ├── omo.yaml │ ├── owl.yaml │ ├── rdf.yaml │ ├── relation_graph.yaml │ ├── ro.yaml │ ├── semsql.yaml │ ├── similarity.yaml │ ├── taxon_constraints.yaml │ └── term_associations.yaml │ ├── loader.py │ ├── ontlib │ ├── README.md │ ├── __init__.py │ ├── common_queries.py │ └── subgraph.py │ ├── sqla │ ├── README.md │ ├── __init__.py │ ├── nlp.py │ ├── obo.py │ ├── omo.py │ ├── owl.py │ ├── rdf.py │ ├── relation_graph.py │ └── semsql.py │ ├── sqlutils │ ├── __init__.py │ ├── reportgen.py │ ├── view2table.py │ └── viewgen.py │ └── utils │ ├── __init__.py │ └── makefile_utils.py ├── tests ├── __init__.py ├── inputs │ ├── go-nucleus.db │ ├── go-nucleus.json │ ├── go-nucleus.owl │ ├── robot-example.db │ └── robot-example.owl ├── integration │ ├── Makefile │ ├── README.md │ └── conf │ │ └── bad-prefixes.csv ├── outputs │ └── README.md ├── test_builder │ ├── __init__.py │ ├── test_builder.py │ └── test_cli.py ├── test_ontlib │ ├── test_common_queries.py │ └── test_subgraph.py ├── test_orm │ ├── 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