├── .cruft.json ├── .github └── workflows │ ├── deploy-docs.yaml │ ├── main.yaml │ └── pypi-publish.yaml ├── .gitignore ├── .pre-commit-config.yaml ├── CONTRIBUTING.md ├── LICENSE ├── Makefile ├── README.md ├── docs ├── Makefile ├── about.rst ├── conf.py ├── explanation │ ├── index.rst │ └── indexing-architecture.md ├── faq.rst ├── how-to │ ├── Calculate-Enrichment.ipynb │ ├── Check-Referential-Integrity.ipynb │ ├── Index-Bioinformatics-Databases.ipynb │ ├── Index-GO-CAMs.ipynb │ ├── Index-Phenopackets.ipynb │ ├── Index-caDSR.ipynb │ ├── Perform-LLM-Inference.ipynb │ ├── Perform-RAG-Inference.ipynb │ ├── Plot-Aggregate-Data.ipynb │ ├── Predict-Missing-Data.ipynb │ ├── Query-Existing-MongoDB.ipynb │ ├── Query-Solr-using-CLI.ipynb │ ├── Query-the-Monarch-KG.ipynb │ ├── Store-an-Ontology.ipynb │ ├── Use-LLM-Indexing.md │ ├── Use-MongoDB.ipynb │ ├── Use-Neo4j.ipynb │ ├── Use-Semantic-Search.ipynb │ ├── Visualize-Embeddings.ipynb │ ├── cadsr │ ├── index.rst │ ├── input │ │ ├── gocam-models-schema.yaml │ │ ├── gocam-models.yaml │ │ ├── gocam-models.yaml.gz │ │ ├── golr.config.yaml │ │ ├── iris-model.png │ │ ├── movies.uml.svg │ │ ├── movies_kg │ │ │ ├── diagrams │ │ │ │ └── MoviesKG.svg │ │ │ ├── edges.csv │ │ │ ├── nodes.csv │ │ │ └── schema.yaml │ │ └── uniprot_caution_cv.csv │ └── up.ddb ├── images │ ├── graph_simple-arr.svg │ ├── neo4j-screenshot-1.png │ └── neo4j-screenshot-2.png ├── index.rst ├── make.bat ├── manual │ └── data-model.ipynb ├── reference │ ├── index-configuration.md │ ├── index.rst │ ├── linkml_store.api.rst │ ├── linkml_store.api.stores.chromadb.chromadb_collection.rst │ ├── linkml_store.api.stores.chromadb.chromadb_database.rst │ ├── linkml_store.api.stores.chromadb.rst │ ├── linkml_store.api.stores.duckdb.duckdb_collection.rst │ ├── linkml_store.api.stores.duckdb.duckdb_database.rst │ ├── linkml_store.api.stores.duckdb.mappings.rst │ ├── linkml_store.api.stores.duckdb.rst │ ├── linkml_store.api.stores.filesystem.filesystem_collection.rst │ ├── linkml_store.api.stores.filesystem.filesystem_database.rst │ ├── linkml_store.api.stores.filesystem.rst │ ├── linkml_store.api.stores.hdf5.hdf5_collection.rst │ ├── linkml_store.api.stores.hdf5.hdf5_database.rst │ ├── linkml_store.api.stores.hdf5.rst │ ├── linkml_store.api.stores.mongodb.mongodb_collection.rst │ ├── linkml_store.api.stores.mongodb.mongodb_database.rst │ ├── linkml_store.api.stores.mongodb.rst │ ├── linkml_store.api.stores.rst │ ├── linkml_store.api.stores.solr.rst │ ├── linkml_store.api.stores.solr.solr_collection.rst │ ├── linkml_store.api.stores.solr.solr_database.rst │ ├── linkml_store.api.stores.solr.solr_utils.rst │ ├── linkml_store.index.rst │ ├── linkml_store.inference.rst │ ├── linkml_store.utils.rst │ └── modules.rst └── tutorials │ ├── Command-Line-Tutorial.ipynb │ ├── Python-Tutorial.ipynb │ ├── go-db.ipynb │ ├── index.rst │ └── input │ └── countries.config.yaml ├── poetry.lock ├── pyproject.toml ├── pytest.ini ├── src ├── linkml_data_browser │ ├── __init__.py │ ├── app.py │ ├── cart.py │ └── state.py └── linkml_store │ ├── __init__.py │ ├── api │ ├── __init__.py │ ├── client.py │ ├── collection.py │ ├── config.py │ ├── database.py │ ├── queries.py │ ├── stores │ │ ├── __init__.py │ │ ├── chromadb │ │ │ ├── __init__.py │ │ │ ├── chromadb_collection.py │ │ │ └── chromadb_database.py │ │ ├── duckdb │ │ │ ├── __init__.py │ │ │ ├── duckdb_collection.py │ │ │ ├── duckdb_database.py │ │ │ └── mappings.py │ │ ├── filesystem │ │ │ ├── __init__.py │ │ │ ├── filesystem_collection.py │ │ │ └── filesystem_database.py │ │ ├── hdf5 │ │ │ ├── __init__.py │ │ │ ├── hdf5_collection.py │ │ │ └── hdf5_database.py │ │ ├── mongodb │ │ │ ├── __init__.py │ │ │ ├── mongodb_collection.py │ │ │ └── mongodb_database.py │ │ ├── neo4j │ │ │ ├── __init__.py │ │ │ ├── neo4j_collection.py │ │ │ └── neo4j_database.py │ │ └── solr │ │ │ ├── __init__.py │ │ │ ├── solr_collection.py │ │ │ ├── solr_database.py │ │ │ └── solr_utils.py │ └── types.py │ ├── cli.py │ ├── constants.py │ ├── graphs │ ├── __init__.py │ └── graph_map.py │ ├── index │ ├── __init__.py │ ├── implementations │ │ ├── __init__.py │ │ ├── llm_indexer.py │ │ └── simple_indexer.py │ └── indexer.py │ ├── inference │ ├── __init__.py │ ├── evaluation.py │ ├── implementations │ │ ├── __init__.py │ │ ├── llm_inference_engine.py │ │ ├── rag_inference_engine.py │ │ ├── rule_based_inference_engine.py │ │ └── sklearn_inference_engine.py │ ├── inference_config.py │ ├── inference_engine.py │ └── inference_engine_registry.py │ ├── plotting │ ├── __init__.py │ ├── cli.py │ ├── dimensionality_reduction.py │ ├── embedding_plot.py │ ├── facet_chart.py │ └── heatmap.py │ ├── utils │ ├── __init__.py │ ├── change_utils.py │ ├── dat_parser.py │ ├── embedding_matcher.py │ ├── embedding_utils.py │ ├── enrichment_analyzer.py │ ├── file_utils.py │ ├── format_utils.py │ ├── io.py │ ├── llm_utils.py │ ├── mongodb_utils.py │ ├── neo4j_utils.py │ ├── object_utils.py │ ├── pandas_utils.py │ ├── patch_utils.py │ ├── query_utils.py │ ├── schema_utils.py │ ├── sklearn_utils.py │ ├── sql_utils.py │ ├── stats_utils.py │ └── vector_utils.py │ └── webapi │ ├── __init__.py │ ├── html │ ├── __init__.py │ ├── base.html.j2 │ ├── collection_details.html.j2 │ ├── database_details.html.j2 │ ├── databases.html.j2 │ └── generic.html.j2 │ └── main.py ├── tests ├── __init__.py ├── conftest.py ├── input │ ├── Phenopacket-001.json │ ├── configurations │ │ └── conf1 │ │ │ └── config.yaml │ ├── countries │ │ ├── countries.config.yaml │ │ ├── countries.jsonl │ │ ├── countries.linkml.yaml │ │ └── routes.csv │ ├── expasy-subset.dat │ ├── iris.csv │ ├── iris.jsonl │ ├── iris.yaml │ ├── llm_cache.db │ ├── movies_kg │ │ └── schema.yaml │ ├── nested-target.yaml │ ├── nested.schema.yaml │ ├── nested.yaml │ ├── nested2.schema.yaml │ ├── schemas │ │ └── phenopackets_linkml │ │ │ ├── any.yaml │ │ │ ├── base.yaml │ │ │ ├── biosample.yaml │ │ │ ├── constants.yaml │ │ │ ├── constants.yaml.old │ │ │ ├── cv_terms.yaml │ │ │ ├── dicts.yaml │ │ │ ├── disease.yaml │ │ │ ├── genome.yaml │ │ │ ├── individual.yaml │ │ │ ├── interpretation.yaml │ │ │ ├── measurement.yaml │ │ │ ├── medical_action.yaml │ │ │ ├── meta_data.yaml │ │ │ ├── pedigree.yaml │ │ │ ├── phenopackets.yaml │ │ │ ├── phenotypic_feature.yaml │ │ │ ├── timestamp.yaml │ │ │ ├── vrs.yaml │ │ │ └── vrsatile.yaml │ ├── test_data │ │ ├── data.csv │ │ ├── data.json │ │ ├── data.tsv │ │ └── data.yaml │ └── uniprot │ │ ├── schema.yaml │ │ ├── uniprot-caution-cv.csv │ │ └── uniprot-comments.tsv ├── test_api │ ├── __init__.py │ ├── test_api.py │ ├── test_filesystem_adapter.py │ ├── test_mongodb_adapter.py │ └── test_neo4j_adapter.py ├── test_bigquery.py ├── test_cli.py ├── test_index │ └── test_index.py ├── test_inference │ ├── __init__.py │ ├── test_rag_engine.py │ ├── test_rule_based_engine.py │ └── test_sklearn_engine.py ├── test_plotting │ ├── __init__.py │ ├── test_clustering.py │ ├── test_duplicates.py │ └── test_heatmap.py └── test_utils │ ├── test_dat_parser.py │ ├── test_enrichment_analyzer.py │ ├── test_format_utils.py │ └── test_object_utils.py └── tox.ini /.cruft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/.cruft.json -------------------------------------------------------------------------------- /.github/workflows/deploy-docs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/.github/workflows/deploy-docs.yaml -------------------------------------------------------------------------------- /.github/workflows/main.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/.github/workflows/main.yaml -------------------------------------------------------------------------------- /.github/workflows/pypi-publish.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/.github/workflows/pypi-publish.yaml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /CONTRIBUTING.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/CONTRIBUTING.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/README.md -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/about.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/about.rst -------------------------------------------------------------------------------- /docs/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/conf.py -------------------------------------------------------------------------------- /docs/explanation/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/explanation/index.rst -------------------------------------------------------------------------------- /docs/explanation/indexing-architecture.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/explanation/indexing-architecture.md -------------------------------------------------------------------------------- /docs/faq.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/faq.rst -------------------------------------------------------------------------------- /docs/how-to/Calculate-Enrichment.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Calculate-Enrichment.ipynb -------------------------------------------------------------------------------- /docs/how-to/Check-Referential-Integrity.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Check-Referential-Integrity.ipynb -------------------------------------------------------------------------------- /docs/how-to/Index-Bioinformatics-Databases.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Index-Bioinformatics-Databases.ipynb -------------------------------------------------------------------------------- /docs/how-to/Index-GO-CAMs.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Index-GO-CAMs.ipynb -------------------------------------------------------------------------------- /docs/how-to/Index-Phenopackets.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Index-Phenopackets.ipynb -------------------------------------------------------------------------------- /docs/how-to/Index-caDSR.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Index-caDSR.ipynb -------------------------------------------------------------------------------- /docs/how-to/Perform-LLM-Inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Perform-LLM-Inference.ipynb -------------------------------------------------------------------------------- /docs/how-to/Perform-RAG-Inference.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Perform-RAG-Inference.ipynb -------------------------------------------------------------------------------- /docs/how-to/Plot-Aggregate-Data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Plot-Aggregate-Data.ipynb -------------------------------------------------------------------------------- /docs/how-to/Predict-Missing-Data.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Predict-Missing-Data.ipynb -------------------------------------------------------------------------------- /docs/how-to/Query-Existing-MongoDB.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Query-Existing-MongoDB.ipynb -------------------------------------------------------------------------------- /docs/how-to/Query-Solr-using-CLI.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Query-Solr-using-CLI.ipynb -------------------------------------------------------------------------------- /docs/how-to/Query-the-Monarch-KG.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Query-the-Monarch-KG.ipynb -------------------------------------------------------------------------------- /docs/how-to/Store-an-Ontology.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Store-an-Ontology.ipynb -------------------------------------------------------------------------------- /docs/how-to/Use-LLM-Indexing.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Use-LLM-Indexing.md -------------------------------------------------------------------------------- /docs/how-to/Use-MongoDB.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Use-MongoDB.ipynb -------------------------------------------------------------------------------- /docs/how-to/Use-Neo4j.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Use-Neo4j.ipynb -------------------------------------------------------------------------------- /docs/how-to/Use-Semantic-Search.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Use-Semantic-Search.ipynb -------------------------------------------------------------------------------- /docs/how-to/Visualize-Embeddings.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/Visualize-Embeddings.ipynb -------------------------------------------------------------------------------- /docs/how-to/cadsr: -------------------------------------------------------------------------------- 1 | /Users/cjm/repos/cde-harmonization/data/cadsr -------------------------------------------------------------------------------- /docs/how-to/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/index.rst -------------------------------------------------------------------------------- /docs/how-to/input/gocam-models-schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/gocam-models-schema.yaml -------------------------------------------------------------------------------- /docs/how-to/input/gocam-models.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/gocam-models.yaml -------------------------------------------------------------------------------- /docs/how-to/input/gocam-models.yaml.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/gocam-models.yaml.gz -------------------------------------------------------------------------------- /docs/how-to/input/golr.config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/golr.config.yaml -------------------------------------------------------------------------------- /docs/how-to/input/iris-model.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/iris-model.png -------------------------------------------------------------------------------- /docs/how-to/input/movies.uml.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/movies.uml.svg -------------------------------------------------------------------------------- /docs/how-to/input/movies_kg/diagrams/MoviesKG.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/movies_kg/diagrams/MoviesKG.svg -------------------------------------------------------------------------------- /docs/how-to/input/movies_kg/edges.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/movies_kg/edges.csv -------------------------------------------------------------------------------- /docs/how-to/input/movies_kg/nodes.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/movies_kg/nodes.csv -------------------------------------------------------------------------------- /docs/how-to/input/movies_kg/schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/movies_kg/schema.yaml -------------------------------------------------------------------------------- /docs/how-to/input/uniprot_caution_cv.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/input/uniprot_caution_cv.csv -------------------------------------------------------------------------------- /docs/how-to/up.ddb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/how-to/up.ddb -------------------------------------------------------------------------------- /docs/images/graph_simple-arr.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/images/graph_simple-arr.svg -------------------------------------------------------------------------------- /docs/images/neo4j-screenshot-1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/images/neo4j-screenshot-1.png -------------------------------------------------------------------------------- /docs/images/neo4j-screenshot-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/images/neo4j-screenshot-2.png -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/index.rst -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/manual/data-model.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/manual/data-model.ipynb -------------------------------------------------------------------------------- /docs/reference/index-configuration.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/index-configuration.md -------------------------------------------------------------------------------- /docs/reference/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/index.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.chromadb.chromadb_collection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.chromadb.chromadb_collection.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.chromadb.chromadb_database.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.chromadb.chromadb_database.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.chromadb.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.chromadb.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.duckdb.duckdb_collection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.duckdb.duckdb_collection.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.duckdb.duckdb_database.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.duckdb.duckdb_database.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.duckdb.mappings.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.duckdb.mappings.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.duckdb.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.duckdb.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.filesystem.filesystem_collection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.filesystem.filesystem_collection.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.filesystem.filesystem_database.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.filesystem.filesystem_database.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.filesystem.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.filesystem.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.hdf5.hdf5_collection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.hdf5.hdf5_collection.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.hdf5.hdf5_database.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.hdf5.hdf5_database.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.hdf5.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.hdf5.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.mongodb.mongodb_collection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.mongodb.mongodb_collection.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.mongodb.mongodb_database.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.mongodb.mongodb_database.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.mongodb.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.mongodb.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.solr.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.solr.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.solr.solr_collection.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.solr.solr_collection.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.solr.solr_database.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.solr.solr_database.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.api.stores.solr.solr_utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.api.stores.solr.solr_utils.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.index.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.inference.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.inference.rst -------------------------------------------------------------------------------- /docs/reference/linkml_store.utils.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/linkml_store.utils.rst -------------------------------------------------------------------------------- /docs/reference/modules.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/reference/modules.rst -------------------------------------------------------------------------------- /docs/tutorials/Command-Line-Tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/tutorials/Command-Line-Tutorial.ipynb -------------------------------------------------------------------------------- /docs/tutorials/Python-Tutorial.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/tutorials/Python-Tutorial.ipynb -------------------------------------------------------------------------------- /docs/tutorials/go-db.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/tutorials/go-db.ipynb -------------------------------------------------------------------------------- /docs/tutorials/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/tutorials/index.rst -------------------------------------------------------------------------------- /docs/tutorials/input/countries.config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/docs/tutorials/input/countries.config.yaml -------------------------------------------------------------------------------- /poetry.lock: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/poetry.lock -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/pyproject.toml -------------------------------------------------------------------------------- /pytest.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/pytest.ini -------------------------------------------------------------------------------- /src/linkml_data_browser/__init__.py: -------------------------------------------------------------------------------- 1 | """linkml-data-browser package.""" 2 | -------------------------------------------------------------------------------- /src/linkml_data_browser/app.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_data_browser/app.py -------------------------------------------------------------------------------- /src/linkml_data_browser/cart.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_data_browser/cart.py -------------------------------------------------------------------------------- /src/linkml_data_browser/state.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_data_browser/state.py -------------------------------------------------------------------------------- /src/linkml_store/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/client.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/client.py -------------------------------------------------------------------------------- /src/linkml_store/api/collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/config.py -------------------------------------------------------------------------------- /src/linkml_store/api/database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/database.py -------------------------------------------------------------------------------- /src/linkml_store/api/queries.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/queries.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/api/stores/chromadb/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/chromadb/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/chromadb/chromadb_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/chromadb/chromadb_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/chromadb/chromadb_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/chromadb/chromadb_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/duckdb/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/duckdb/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/duckdb/duckdb_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/duckdb/duckdb_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/duckdb/duckdb_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/duckdb/duckdb_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/duckdb/mappings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/duckdb/mappings.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/filesystem/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/filesystem/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/filesystem/filesystem_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/filesystem/filesystem_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/filesystem/filesystem_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/filesystem/filesystem_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/hdf5/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/hdf5/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/hdf5/hdf5_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/hdf5/hdf5_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/hdf5/hdf5_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/hdf5/hdf5_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/mongodb/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/mongodb/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/mongodb/mongodb_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/mongodb/mongodb_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/mongodb/mongodb_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/mongodb/mongodb_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/neo4j/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/api/stores/neo4j/neo4j_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/neo4j/neo4j_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/neo4j/neo4j_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/neo4j/neo4j_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/solr/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Wrapper for Solr endpoints. 3 | """ 4 | -------------------------------------------------------------------------------- /src/linkml_store/api/stores/solr/solr_collection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/solr/solr_collection.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/solr/solr_database.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/stores/solr/solr_database.py -------------------------------------------------------------------------------- /src/linkml_store/api/stores/solr/solr_utils.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/api/types.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/api/types.py -------------------------------------------------------------------------------- /src/linkml_store/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/cli.py -------------------------------------------------------------------------------- /src/linkml_store/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/constants.py -------------------------------------------------------------------------------- /src/linkml_store/graphs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/graphs/graph_map.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/graphs/graph_map.py -------------------------------------------------------------------------------- /src/linkml_store/index/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/index/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/index/implementations/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/index/implementations/llm_indexer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/index/implementations/llm_indexer.py -------------------------------------------------------------------------------- /src/linkml_store/index/implementations/simple_indexer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/index/implementations/simple_indexer.py -------------------------------------------------------------------------------- /src/linkml_store/index/indexer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/index/indexer.py -------------------------------------------------------------------------------- /src/linkml_store/inference/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/inference/evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/evaluation.py -------------------------------------------------------------------------------- /src/linkml_store/inference/implementations/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/inference/implementations/llm_inference_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/implementations/llm_inference_engine.py -------------------------------------------------------------------------------- /src/linkml_store/inference/implementations/rag_inference_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/implementations/rag_inference_engine.py -------------------------------------------------------------------------------- /src/linkml_store/inference/implementations/rule_based_inference_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/implementations/rule_based_inference_engine.py -------------------------------------------------------------------------------- /src/linkml_store/inference/implementations/sklearn_inference_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/implementations/sklearn_inference_engine.py -------------------------------------------------------------------------------- /src/linkml_store/inference/inference_config.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/inference_config.py -------------------------------------------------------------------------------- /src/linkml_store/inference/inference_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/inference_engine.py -------------------------------------------------------------------------------- /src/linkml_store/inference/inference_engine_registry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/inference/inference_engine_registry.py -------------------------------------------------------------------------------- /src/linkml_store/plotting/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/plotting/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/plotting/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/plotting/cli.py -------------------------------------------------------------------------------- /src/linkml_store/plotting/dimensionality_reduction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/plotting/dimensionality_reduction.py -------------------------------------------------------------------------------- /src/linkml_store/plotting/embedding_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/plotting/embedding_plot.py -------------------------------------------------------------------------------- /src/linkml_store/plotting/facet_chart.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/plotting/facet_chart.py -------------------------------------------------------------------------------- /src/linkml_store/plotting/heatmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/plotting/heatmap.py -------------------------------------------------------------------------------- /src/linkml_store/utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/utils/change_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/change_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/dat_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/dat_parser.py -------------------------------------------------------------------------------- /src/linkml_store/utils/embedding_matcher.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/embedding_matcher.py -------------------------------------------------------------------------------- /src/linkml_store/utils/embedding_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/embedding_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/enrichment_analyzer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/enrichment_analyzer.py -------------------------------------------------------------------------------- /src/linkml_store/utils/file_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/file_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/format_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/format_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/io.py -------------------------------------------------------------------------------- /src/linkml_store/utils/llm_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/llm_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/mongodb_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/mongodb_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/neo4j_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/neo4j_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/object_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/object_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/pandas_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/pandas_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/patch_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/patch_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/query_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/query_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/schema_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/schema_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/sklearn_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/sklearn_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/sql_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/sql_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/stats_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/stats_utils.py -------------------------------------------------------------------------------- /src/linkml_store/utils/vector_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/utils/vector_utils.py -------------------------------------------------------------------------------- /src/linkml_store/webapi/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/linkml_store/webapi/html/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/html/__init__.py -------------------------------------------------------------------------------- /src/linkml_store/webapi/html/base.html.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/html/base.html.j2 -------------------------------------------------------------------------------- /src/linkml_store/webapi/html/collection_details.html.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/html/collection_details.html.j2 -------------------------------------------------------------------------------- /src/linkml_store/webapi/html/database_details.html.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/html/database_details.html.j2 -------------------------------------------------------------------------------- /src/linkml_store/webapi/html/databases.html.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/html/databases.html.j2 -------------------------------------------------------------------------------- /src/linkml_store/webapi/html/generic.html.j2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/html/generic.html.j2 -------------------------------------------------------------------------------- /src/linkml_store/webapi/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/src/linkml_store/webapi/main.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/__init__.py -------------------------------------------------------------------------------- /tests/conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/conftest.py -------------------------------------------------------------------------------- /tests/input/Phenopacket-001.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/Phenopacket-001.json -------------------------------------------------------------------------------- /tests/input/configurations/conf1/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/configurations/conf1/config.yaml -------------------------------------------------------------------------------- /tests/input/countries/countries.config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/countries/countries.config.yaml -------------------------------------------------------------------------------- /tests/input/countries/countries.jsonl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/countries/countries.jsonl -------------------------------------------------------------------------------- /tests/input/countries/countries.linkml.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/countries/countries.linkml.yaml -------------------------------------------------------------------------------- /tests/input/countries/routes.csv: -------------------------------------------------------------------------------- 1 | origin,destination,method 2 | DE,FR,rail -------------------------------------------------------------------------------- /tests/input/expasy-subset.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/expasy-subset.dat -------------------------------------------------------------------------------- /tests/input/iris.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/iris.csv -------------------------------------------------------------------------------- /tests/input/iris.jsonl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/iris.jsonl -------------------------------------------------------------------------------- /tests/input/iris.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/iris.yaml -------------------------------------------------------------------------------- /tests/input/llm_cache.db: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/llm_cache.db -------------------------------------------------------------------------------- /tests/input/movies_kg/schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/movies_kg/schema.yaml -------------------------------------------------------------------------------- /tests/input/nested-target.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/nested-target.yaml -------------------------------------------------------------------------------- /tests/input/nested.schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/nested.schema.yaml -------------------------------------------------------------------------------- /tests/input/nested.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/nested.yaml -------------------------------------------------------------------------------- /tests/input/nested2.schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/nested2.schema.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/any.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/any.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/base.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/base.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/biosample.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/biosample.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/constants.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/constants.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/constants.yaml.old: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/constants.yaml.old -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/cv_terms.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/cv_terms.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/dicts.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/dicts.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/disease.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/disease.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/genome.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/genome.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/individual.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/individual.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/interpretation.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/interpretation.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/measurement.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/measurement.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/medical_action.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/medical_action.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/meta_data.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/meta_data.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/pedigree.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/pedigree.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/phenopackets.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/phenopackets.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/phenotypic_feature.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/phenotypic_feature.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/timestamp.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/timestamp.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/vrs.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/vrs.yaml -------------------------------------------------------------------------------- /tests/input/schemas/phenopackets_linkml/vrsatile.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/schemas/phenopackets_linkml/vrsatile.yaml -------------------------------------------------------------------------------- /tests/input/test_data/data.csv: -------------------------------------------------------------------------------- 1 | id,name,age 2 | 1,John,30 3 | 2,Alice,25 4 | 3,Bob,35 5 | -------------------------------------------------------------------------------- /tests/input/test_data/data.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/test_data/data.json -------------------------------------------------------------------------------- /tests/input/test_data/data.tsv: -------------------------------------------------------------------------------- 1 | id name age 2 | 1 John 30 3 | 2 Alice 25 4 | 3 Bob 35 5 | -------------------------------------------------------------------------------- /tests/input/test_data/data.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/test_data/data.yaml -------------------------------------------------------------------------------- /tests/input/uniprot/schema.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/uniprot/schema.yaml -------------------------------------------------------------------------------- /tests/input/uniprot/uniprot-caution-cv.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/uniprot/uniprot-caution-cv.csv -------------------------------------------------------------------------------- /tests/input/uniprot/uniprot-comments.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/input/uniprot/uniprot-comments.tsv -------------------------------------------------------------------------------- /tests/test_api/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/test_api/test_api.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_api/test_api.py -------------------------------------------------------------------------------- /tests/test_api/test_filesystem_adapter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_api/test_filesystem_adapter.py -------------------------------------------------------------------------------- /tests/test_api/test_mongodb_adapter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_api/test_mongodb_adapter.py -------------------------------------------------------------------------------- /tests/test_api/test_neo4j_adapter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_api/test_neo4j_adapter.py -------------------------------------------------------------------------------- /tests/test_bigquery.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_bigquery.py -------------------------------------------------------------------------------- /tests/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_cli.py -------------------------------------------------------------------------------- /tests/test_index/test_index.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_index/test_index.py -------------------------------------------------------------------------------- /tests/test_inference/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_inference/__init__.py -------------------------------------------------------------------------------- /tests/test_inference/test_rag_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_inference/test_rag_engine.py -------------------------------------------------------------------------------- /tests/test_inference/test_rule_based_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_inference/test_rule_based_engine.py -------------------------------------------------------------------------------- /tests/test_inference/test_sklearn_engine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_inference/test_sklearn_engine.py -------------------------------------------------------------------------------- /tests/test_plotting/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Tests for the plotting package. 3 | """ -------------------------------------------------------------------------------- /tests/test_plotting/test_clustering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_plotting/test_clustering.py -------------------------------------------------------------------------------- /tests/test_plotting/test_duplicates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_plotting/test_duplicates.py -------------------------------------------------------------------------------- /tests/test_plotting/test_heatmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_plotting/test_heatmap.py -------------------------------------------------------------------------------- /tests/test_utils/test_dat_parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_utils/test_dat_parser.py -------------------------------------------------------------------------------- /tests/test_utils/test_enrichment_analyzer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_utils/test_enrichment_analyzer.py -------------------------------------------------------------------------------- /tests/test_utils/test_format_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_utils/test_format_utils.py -------------------------------------------------------------------------------- /tests/test_utils/test_object_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tests/test_utils/test_object_utils.py -------------------------------------------------------------------------------- /tox.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/linkml/linkml-store/HEAD/tox.ini --------------------------------------------------------------------------------