LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
docs/bulk_prefix_request_template.tsv
docs/img/bibliography_years.svg
docs/img/bioregistry_coverage.svg
docs/img/bioregistry_coverage_bar.svg
docs/img/bioregistry_coverage_bar_short.svg
docs/img/datamodel_umls.svg
docs/img/external_overlap.svg
docs/img/has_attribute.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/deployment.rst
docs/source/index.rst
docs/source/logo.png
docs/source/pandas.rst
docs/source/reference.rst
src/bioregistry/__init__.py
src/bioregistry/__main__.py
src/bioregistry/bibliometrics.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/pandas.py
src/bioregistry/parse_iri.py
src/bioregistry/parse_version_iri.py
src/bioregistry/py.typed
src/bioregistry/record_accumulator.py
src/bioregistry/resolve.py
src/bioregistry/resolve_identifier.py
src/bioregistry/resource_manager.py
src/bioregistry/schema_utils.py
src/bioregistry/summary.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/aberowl.py
src/bioregistry/align/agroportal.py
src/bioregistry/align/bartoc.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/cropoct.py
src/bioregistry/align/ecoportal.py
src/bioregistry/align/edam.py
src/bioregistry/align/fairsharing.py
src/bioregistry/align/go.py
src/bioregistry/align/hl7.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/re3data.py
src/bioregistry/align/uniprot.py
src/bioregistry/align/utils.py
src/bioregistry/align/wikidata.py
src/bioregistry/analysis/__init__.py
src/bioregistry/analysis/title_tfidf.py
src/bioregistry/app/__init__.py
src/bioregistry/app/api.py
src/bioregistry/app/cli.py
src/bioregistry/app/constants.py
src/bioregistry/app/impl.py
src/bioregistry/app/proxies.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/highlights/keywords.html
src/bioregistry/app/templates/highlights/owners.html
src/bioregistry/app/templates/highlights/relations.html
src/bioregistry/app/templates/highlights/twitter.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/benchmarks/__init__.py
src/bioregistry/benchmarks/__main__.py
src/bioregistry/benchmarks/cli.py
src/bioregistry/benchmarks/curie_parsing.py
src/bioregistry/benchmarks/curie_validation.py
src/bioregistry/benchmarks/uri_parsing.py
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/bulk_import.py
src/bioregistry/curation/clean_licenses.py
src/bioregistry/curation/clean_name_suffixes.py
src/bioregistry/curation/clean_publications.py
src/bioregistry/curation/cleanup_authors.py
src/bioregistry/curation/deprecation_diff.py
src/bioregistry/curation/enrich_publications.py
src/bioregistry/curation/import_pc_semiautomatic.py
src/bioregistry/curation/make_description_curation_sheet.py
src/bioregistry/curation/map_bartoc_via_wikidata.py
src/bioregistry/curation/map_re3data_via_fairsharing.py
src/bioregistry/curation/rename_metaprefix.py
src/bioregistry/curation/review_pc.py
src/bioregistry/curation/suggest_author_curation.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/aberowl/curation.tsv
src/bioregistry/data/external/aberowl/processed.json
src/bioregistry/data/external/agroportal/curation.tsv
src/bioregistry/data/external/agroportal/processed.json
src/bioregistry/data/external/agroportal/raw.json
src/bioregistry/data/external/bartoc/curation.tsv
src/bioregistry/data/external/bartoc/processed.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/processed.json
src/bioregistry/data/external/cropoct/curation.tsv
src/bioregistry/data/external/cropoct/processed.json
src/bioregistry/data/external/cropoct/raw.yaml
src/bioregistry/data/external/ecoportal/curation.tsv
src/bioregistry/data/external/ecoportal/processed.json
src/bioregistry/data/external/ecoportal/raw.json
src/bioregistry/data/external/edam/curation.tsv
src/bioregistry/data/external/edam/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/hl7/curation.tsv
src/bioregistry/data/external/miriam/processed.json
src/bioregistry/data/external/miriam/raw.json
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/processed.json
src/bioregistry/data/external/obofoundry/raw.yaml
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/ontobee/raw.html
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/re3data/curation.tsv
src/bioregistry/data/external/re3data/processed.json
src/bioregistry/data/external/uniprot/curation.tsv
src/bioregistry/data/external/uniprot/processed.json
src/bioregistry/data/external/uniprot/raw.json
src/bioregistry/data/external/wikidata/curation.tsv
src/bioregistry/data/external/wikidata/processed.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/tables_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/aberowl.py
src/bioregistry/external/bartoc.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/cropoct.py
src/bioregistry/external/edam.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/re3data.py
src/bioregistry/external/uniprot.py
src/bioregistry/external/wikidata.py
src/bioregistry/external/hl7/OID_Report.csv
src/bioregistry/external/hl7/__init__.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_api.py
tests/test_collections.py
tests/test_contexts.py
tests/test_data.py
tests/test_data_slow.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_pandas.py
tests/test_resolve.py
tests/test_sparql.py
tests/test_usages.py
tests/test_utils.py
tests/test_web/__init__.py
tests/test_web/test_api.py
tests/test_web/test_ui.py