LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
docs/bulk_prefix_request_template.tsv
docs/img/bioregistry_coverage.svg
docs/img/bioregistry_coverage_bar.svg
docs/img/bioregistry_coverage_bar_short.svg
docs/img/external_overlap.svg
docs/img/has_attribute.svg
docs/img/licenses.svg
docs/img/providers.svg
docs/img/regex_report.svg
docs/img/xrefs.svg
docs/source/alignment.rst
docs/source/cli.rst
docs/source/conf.py
docs/source/index.rst
docs/source/logo.png
docs/source/reference.rst
docs/source/api/bioregistry.Author.rst
docs/source/api/bioregistry.Collection.rst
docs/source/api/bioregistry.Context.rst
docs/source/api/bioregistry.Manager.rst
docs/source/api/bioregistry.Provider.rst
docs/source/api/bioregistry.Registry.rst
docs/source/api/bioregistry.Resource.rst
docs/source/api/bioregistry.align.Aligner.rst
docs/source/api/bioregistry.align.BioContextAligner.rst
docs/source/api/bioregistry.align.BioPortalAligner.rst
docs/source/api/bioregistry.align.BiolinkAligner.rst
docs/source/api/bioregistry.align.CellosaurusAligner.rst
docs/source/api/bioregistry.align.ChemInfAligner.rst
docs/source/api/bioregistry.align.FairsharingAligner.rst
docs/source/api/bioregistry.align.GoAligner.rst
docs/source/api/bioregistry.align.MiriamAligner.rst
docs/source/api/bioregistry.align.N2TAligner.rst
docs/source/api/bioregistry.align.NcbiAligner.rst
docs/source/api/bioregistry.align.OBOFoundryAligner.rst
docs/source/api/bioregistry.align.OLSAligner.rst
docs/source/api/bioregistry.align.OntobeeAligner.rst
docs/source/api/bioregistry.align.PrefixCommonsAligner.rst
docs/source/api/bioregistry.align.UniProtAligner.rst
docs/source/api/bioregistry.align.WikidataAligner.rst
docs/source/api/bioregistry.curie_from_iri.rst
docs/source/api/bioregistry.external.get_biocontext.rst
docs/source/api/bioregistry.external.get_biolink.rst
docs/source/api/bioregistry.external.get_bioportal.rst
docs/source/api/bioregistry.external.get_cellosaurus.rst
docs/source/api/bioregistry.external.get_cheminf.rst
docs/source/api/bioregistry.external.get_fairsharing.rst
docs/source/api/bioregistry.external.get_go.rst
docs/source/api/bioregistry.external.get_miriam.rst
docs/source/api/bioregistry.external.get_n2t.rst
docs/source/api/bioregistry.external.get_ncbi.rst
docs/source/api/bioregistry.external.get_obofoundry.rst
docs/source/api/bioregistry.external.get_ols.rst
docs/source/api/bioregistry.external.get_ontobee.rst
docs/source/api/bioregistry.external.get_prefixcommons.rst
docs/source/api/bioregistry.external.get_uniprot.rst
docs/source/api/bioregistry.external.get_wikidata.rst
docs/source/api/bioregistry.get_appears_in.rst
docs/source/api/bioregistry.get_banana.rst
docs/source/api/bioregistry.get_biocontext_uri_format.rst
docs/source/api/bioregistry.get_bioportal_iri.rst
docs/source/api/bioregistry.get_bioportal_prefix.rst
docs/source/api/bioregistry.get_bioregistry_iri.rst
docs/source/api/bioregistry.get_canonical_for.rst
docs/source/api/bioregistry.get_collection.rst
docs/source/api/bioregistry.get_contact.rst
docs/source/api/bioregistry.get_contact_email.rst
docs/source/api/bioregistry.get_contact_github.rst
docs/source/api/bioregistry.get_contact_name.rst
docs/source/api/bioregistry.get_contact_orcid.rst
docs/source/api/bioregistry.get_context.rst
docs/source/api/bioregistry.get_curie_pattern.rst
docs/source/api/bioregistry.get_default_format.rst
docs/source/api/bioregistry.get_default_iri.rst
docs/source/api/bioregistry.get_depends_on.rst
docs/source/api/bioregistry.get_description.rst
docs/source/api/bioregistry.get_example.rst
docs/source/api/bioregistry.get_external.rst
docs/source/api/bioregistry.get_fairsharing_prefix.rst
docs/source/api/bioregistry.get_has_canonical.rst
docs/source/api/bioregistry.get_has_parts.rst
docs/source/api/bioregistry.get_homepage.rst
docs/source/api/bioregistry.get_identifiers_org_curie.rst
docs/source/api/bioregistry.get_identifiers_org_iri.rst
docs/source/api/bioregistry.get_identifiers_org_prefix.rst
docs/source/api/bioregistry.get_iri.rst
docs/source/api/bioregistry.get_json_download.rst
docs/source/api/bioregistry.get_license.rst
docs/source/api/bioregistry.get_license_conflicts.rst
docs/source/api/bioregistry.get_link.rst
docs/source/api/bioregistry.get_mappings.rst
docs/source/api/bioregistry.get_miriam_uri_format.rst
docs/source/api/bioregistry.get_miriam_uri_prefix.rst
docs/source/api/bioregistry.get_n2t_iri.rst
docs/source/api/bioregistry.get_n2t_prefix.rst
docs/source/api/bioregistry.get_name.rst
docs/source/api/bioregistry.get_namespace_in_lui.rst
docs/source/api/bioregistry.get_obo_download.rst
docs/source/api/bioregistry.get_obo_health_url.rst
docs/source/api/bioregistry.get_obofoundry_iri.rst
docs/source/api/bioregistry.get_obofoundry_prefix.rst
docs/source/api/bioregistry.get_obofoundry_uri_format.rst
docs/source/api/bioregistry.get_obofoundry_uri_prefix.rst
docs/source/api/bioregistry.get_ols_iri.rst
docs/source/api/bioregistry.get_ols_prefix.rst
docs/source/api/bioregistry.get_ols_uri_format.rst
docs/source/api/bioregistry.get_ols_uri_prefix.rst
docs/source/api/bioregistry.get_owl_download.rst
docs/source/api/bioregistry.get_part_of.rst
docs/source/api/bioregistry.get_pattern.rst
docs/source/api/bioregistry.get_pattern_map.rst
docs/source/api/bioregistry.get_preferred_prefix.rst
docs/source/api/bioregistry.get_prefix_map.rst
docs/source/api/bioregistry.get_prefixcommons_uri_format.rst
docs/source/api/bioregistry.get_provided_by.rst
docs/source/api/bioregistry.get_providers.rst
docs/source/api/bioregistry.get_providers_list.rst
docs/source/api/bioregistry.get_provides_for.rst
docs/source/api/bioregistry.get_registry.rst
docs/source/api/bioregistry.get_registry_description.rst
docs/source/api/bioregistry.get_registry_example.rst
docs/source/api/bioregistry.get_registry_homepage.rst
docs/source/api/bioregistry.get_registry_invmap.rst
docs/source/api/bioregistry.get_registry_map.rst
docs/source/api/bioregistry.get_registry_name.rst
docs/source/api/bioregistry.get_registry_provider_uri_format.rst
docs/source/api/bioregistry.get_registry_short_name.rst
docs/source/api/bioregistry.get_registry_uri.rst
docs/source/api/bioregistry.get_repository.rst
docs/source/api/bioregistry.get_resource.rst
docs/source/api/bioregistry.get_synonyms.rst
docs/source/api/bioregistry.get_uri_format.rst
docs/source/api/bioregistry.get_uri_prefix.rst
docs/source/api/bioregistry.get_version.rst
docs/source/api/bioregistry.get_versions.rst
docs/source/api/bioregistry.get_wikidata_prefix.rst
docs/source/api/bioregistry.has_no_terms.rst
docs/source/api/bioregistry.is_deprecated.rst
docs/source/api/bioregistry.is_known_identifier.rst
docs/source/api/bioregistry.is_mismatch.rst
docs/source/api/bioregistry.is_proprietary.rst
docs/source/api/bioregistry.normalize_curie.rst
docs/source/api/bioregistry.normalize_parsed_curie.rst
docs/source/api/bioregistry.normalize_prefix.rst
docs/source/api/bioregistry.parse_curie.rst
docs/source/api/bioregistry.parse_iri.rst
docs/source/api/bioregistry.parse_obolibrary_purl.rst
docs/source/api/bioregistry.read_collections.rst
docs/source/api/bioregistry.read_contexts.rst
docs/source/api/bioregistry.read_contributors.rst
docs/source/api/bioregistry.read_metaregistry.rst
docs/source/api/bioregistry.read_mismatches.rst
docs/source/api/bioregistry.read_registry.rst
docs/source/api/bioregistry.write_contexts.rst
docs/source/api/bioregistry.write_registry.rst
src/bioregistry/__init__.py
src/bioregistry/__main__.py
src/bioregistry/cli.py
src/bioregistry/collection_api.py
src/bioregistry/compare.py
src/bioregistry/constants.py
src/bioregistry/license_standardizer.py
src/bioregistry/lint.py
src/bioregistry/metaresource_api.py
src/bioregistry/parse_iri.py
src/bioregistry/py.typed
src/bioregistry/resolve.py
src/bioregistry/resolve_identifier.py
src/bioregistry/resource_manager.py
src/bioregistry/schema_utils.py
src/bioregistry/upload_ndex.py
src/bioregistry/uri_format.py
src/bioregistry/utils.py
src/bioregistry/version.py
src/bioregistry.egg-info/PKG-INFO
src/bioregistry.egg-info/SOURCES.txt
src/bioregistry.egg-info/dependency_links.txt
src/bioregistry.egg-info/entry_points.txt
src/bioregistry.egg-info/not-zip-safe
src/bioregistry.egg-info/requires.txt
src/bioregistry.egg-info/top_level.txt
src/bioregistry/align/__init__.py
src/bioregistry/align/biocontext.py
src/bioregistry/align/biolink.py
src/bioregistry/align/bioportal.py
src/bioregistry/align/cellosaurus.py
src/bioregistry/align/cheminf.py
src/bioregistry/align/fairsharing.py
src/bioregistry/align/go.py
src/bioregistry/align/miriam.py
src/bioregistry/align/n2t.py
src/bioregistry/align/ncbi.py
src/bioregistry/align/obofoundry.py
src/bioregistry/align/ols.py
src/bioregistry/align/ontobee.py
src/bioregistry/align/prefixcommons.py
src/bioregistry/align/uniprot.py
src/bioregistry/align/utils.py
src/bioregistry/align/wikidata.py
src/bioregistry/app/__init__.py
src/bioregistry/app/api.py
src/bioregistry/app/test.py
src/bioregistry/app/ui.py
src/bioregistry/app/utils.py
src/bioregistry/app/wsgi.py
src/bioregistry/app/static/logo.svg
src/bioregistry/app/templates/base.html
src/bioregistry/app/templates/collection.html
src/bioregistry/app/templates/collections.html
src/bioregistry/app/templates/context.html
src/bioregistry/app/templates/contexts.html
src/bioregistry/app/templates/contributor.html
src/bioregistry/app/templates/contributors.html
src/bioregistry/app/templates/home.html
src/bioregistry/app/templates/macros.html
src/bioregistry/app/templates/metaresource.html
src/bioregistry/app/templates/metaresources.html
src/bioregistry/app/templates/prose.html
src/bioregistry/app/templates/reference.html
src/bioregistry/app/templates/resource.html
src/bioregistry/app/templates/resources.html
src/bioregistry/app/templates/meta/access.html
src/bioregistry/app/templates/meta/acknowledgements.html
src/bioregistry/app/templates/meta/download.html
src/bioregistry/app/templates/meta/related.html
src/bioregistry/app/templates/meta/schema.html
src/bioregistry/app/templates/meta/summary.html
src/bioregistry/app/templates/meta/sustainability.html
src/bioregistry/app/templates/resolve_errors/disallowed_identifier.html
src/bioregistry/app/templates/resolve_errors/invalid_identifier.html
src/bioregistry/app/templates/resolve_errors/missing_prefix.html
src/bioregistry/app/templates/resolve_errors/missing_providers.html
src/bioregistry/curation/__init__.py
src/bioregistry/curation/add_co_providers.py
src/bioregistry/curation/add_descriptions_from_gs.py
src/bioregistry/curation/add_examples.py
src/bioregistry/curation/add_examples_from_javert.py
src/bioregistry/curation/add_examples_from_ols.py
src/bioregistry/curation/add_ontology_regexes.py
src/bioregistry/curation/clean_name_suffixes.py
src/bioregistry/curation/deprecation_diff.py
src/bioregistry/curation/make_description_curation_sheet.py
src/bioregistry/curation/rename_metaprefix.py
src/bioregistry/curation/suggest_uniprot_providers.py
src/bioregistry/data/README.md
src/bioregistry/data/__init__.py
src/bioregistry/data/bioregistry.json
src/bioregistry/data/collections.json
src/bioregistry/data/contexts.json
src/bioregistry/data/metaregistry.json
src/bioregistry/data/mismatch.json
src/bioregistry/data/processing_biolink.json
src/bioregistry/data/processing_go.json
src/bioregistry/data/processing_ols.json
src/bioregistry/data/processing_wikidata.json
src/bioregistry/data/external/biocontext/curation.tsv
src/bioregistry/data/external/biocontext/processed.json
src/bioregistry/data/external/biocontext/raw.json
src/bioregistry/data/external/biolink/curation.tsv
src/bioregistry/data/external/biolink/processed.json
src/bioregistry/data/external/biolink/raw.yaml
src/bioregistry/data/external/bioportal/curation.tsv
src/bioregistry/data/external/bioportal/processed.json
src/bioregistry/data/external/bioportal/raw.json
src/bioregistry/data/external/cellosaurus/curation.tsv
src/bioregistry/data/external/cellosaurus/processed.json
src/bioregistry/data/external/cellosaurus/raw.txt
src/bioregistry/data/external/cheminf/curation.tsv
src/bioregistry/data/external/cheminf/processed.json
src/bioregistry/data/external/fairsharing/README.md
src/bioregistry/data/external/fairsharing/curation.tsv
src/bioregistry/data/external/fairsharing/processed.json
src/bioregistry/data/external/go/curation.tsv
src/bioregistry/data/external/go/processed.json
src/bioregistry/data/external/go/raw.yml
src/bioregistry/data/external/miriam/curation.tsv
src/bioregistry/data/external/miriam/processed.json
src/bioregistry/data/external/miriam/raw.json
src/bioregistry/data/external/n2t/curation.tsv
src/bioregistry/data/external/n2t/processed.json
src/bioregistry/data/external/n2t/raw.yml
src/bioregistry/data/external/ncbi/curation.tsv
src/bioregistry/data/external/ncbi/processed.json
src/bioregistry/data/external/ncbi/raw.html
src/bioregistry/data/external/obofoundry/curation.tsv
src/bioregistry/data/external/obofoundry/processed.json
src/bioregistry/data/external/obofoundry/raw.yaml
src/bioregistry/data/external/ols/curation.tsv
src/bioregistry/data/external/ols/processed.json
src/bioregistry/data/external/ols/raw.json
src/bioregistry/data/external/ontobee/curation.tsv
src/bioregistry/data/external/ontobee/processed.json
src/bioregistry/data/external/prefixcommons/curation.tsv
src/bioregistry/data/external/prefixcommons/processed.json
src/bioregistry/data/external/prefixcommons/raw.tsv
src/bioregistry/data/external/uniprot/curation.tsv
src/bioregistry/data/external/uniprot/processed.json
src/bioregistry/data/external/uniprot/raw.xml
src/bioregistry/data/external/uniprot/uniprot.json
src/bioregistry/data/external/uniprot/uniprot.xml
src/bioregistry/data/external/wikidata/curation.tsv
src/bioregistry/data/external/wikidata/processed.json
src/bioregistry/data/external/wikidata/raw.json
src/bioregistry/export/__init__.py
src/bioregistry/export/__main__.py
src/bioregistry/export/cli.py
src/bioregistry/export/prefix_maps.py
src/bioregistry/export/rdf_export.py
src/bioregistry/export/schema_export.py
src/bioregistry/export/sssom_export.py
src/bioregistry/export/tsv_export.py
src/bioregistry/export/warnings_export.py
src/bioregistry/export/yaml_export.py
src/bioregistry/external/__init__.py
src/bioregistry/external/biocontext.py
src/bioregistry/external/biolink.py
src/bioregistry/external/bioportal.py
src/bioregistry/external/cellosaurus.py
src/bioregistry/external/cheminf.py
src/bioregistry/external/fairsharing.py
src/bioregistry/external/go.py
src/bioregistry/external/miriam.py
src/bioregistry/external/n2t.py
src/bioregistry/external/ncbi.py
src/bioregistry/external/obofoundry.py
src/bioregistry/external/ols.py
src/bioregistry/external/ontobee.py
src/bioregistry/external/prefixcommons.py
src/bioregistry/external/uniprot.py
src/bioregistry/external/wikidata.py
src/bioregistry/gh/__init__.py
src/bioregistry/gh/github_client.py
src/bioregistry/gh/new_prefix.py
src/bioregistry/health/__init__.py
src/bioregistry/health/__main__.py
src/bioregistry/health/check_homepages.py
src/bioregistry/health/check_providers.py
src/bioregistry/health/cli.py
src/bioregistry/schema/__init__.py
src/bioregistry/schema/constants.py
src/bioregistry/schema/schema.json
src/bioregistry/schema/struct.py
src/bioregistry/schema/utils.py
tests/__init__.py
tests/test_acquisition.py
tests/test_collections.py
tests/test_contexts.py
tests/test_data.py
tests/test_duplicates.py
tests/test_identifiers_org.py
tests/test_indra.py
tests/test_manager.py
tests/test_metaregistry.py
tests/test_obofoundry.py
tests/test_ols.py
tests/test_resolve.py
tests/test_web.py