├── .github ├── ISSUE_TEMPLATE │ ├── add-collection-prefix.yml │ ├── add-new-collection.md │ ├── merge.yml │ ├── mismatch.yml │ ├── new-prefix.yml │ ├── new-provider.yml │ ├── update-misc.yml │ └── update-regex.yml └── workflows │ ├── deploy.yml │ ├── docker.yml │ ├── health.yml │ ├── new_prefix_pr.yml │ ├── paper_ranking.yml │ ├── release.yml │ ├── service_test.yml │ ├── tests.yml │ ├── update.yml │ └── update_prefix_cc.yml ├── .gitignore ├── .readthedocs.yml ├── CITATION.cff ├── Dockerfile ├── LICENSE ├── README.md ├── docker-compose.yml ├── docs ├── .well-known │ └── funding-manifest-urls ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── GOVERNANCE.md ├── README.md ├── _config.yml ├── _data │ ├── curation.yml │ ├── health.yaml │ ├── usages.yml │ └── warnings.yml ├── bulk_prefix_request_template.tsv ├── curation-blacklisting-external.md ├── curation-import-external.md ├── curation.md ├── datamodel.md ├── glossary.md ├── guides │ ├── README.md │ ├── literature_curation.md │ ├── mapping_review.md │ ├── providers.md │ └── publications.md ├── health.md ├── img │ ├── bibliography_years.svg │ ├── bioregistry_coverage.svg │ ├── bioregistry_coverage_bar.svg │ ├── bioregistry_coverage_bar_short.svg │ ├── datamodel_umls.png │ ├── datamodel_umls.svg │ ├── external_overlap.svg │ ├── has_attribute.svg │ ├── providers.svg │ ├── regex_report.svg │ └── xrefs.svg ├── index.md ├── source │ ├── alignment.rst │ ├── cli.rst │ ├── conf.py │ ├── curation.rst │ ├── deployment.rst │ ├── index.rst │ ├── logo.png │ ├── pandas.rst │ ├── reference.rst │ ├── references.rst │ └── validation-cli.rst ├── users.md └── warnings.md ├── exports ├── README.md ├── alignment │ ├── aberowl.tsv │ ├── agroportal.tsv │ ├── bartoc.tsv │ ├── biocontext.tsv │ ├── biolink.tsv │ ├── bioportal.tsv │ ├── cellosaurus.tsv │ ├── cheminf.tsv │ ├── cropoct.tsv │ ├── ecoportal.tsv │ ├── edam.tsv │ ├── fairsharing.tsv │ ├── go.tsv │ ├── hl7.tsv │ ├── integbio.tsv │ ├── lov.tsv │ ├── ncbi.tsv │ ├── ontobee.tsv │ ├── pathguide.tsv │ ├── prefixcommons.tsv │ ├── re3data.tsv │ ├── togoid.tsv │ ├── uniprot.tsv │ ├── wikidata.tsv │ └── zazuko.tsv ├── analyses │ ├── README.md │ ├── mapping_checking │ │ ├── README.md │ │ ├── mapping_checking_workflow.png │ │ └── mapping_embedding_similarities.tsv │ └── paper_ranking │ │ ├── README.md │ │ ├── evaluation.tsv │ │ ├── importances.tsv │ │ ├── outline.png │ │ └── predictions.tsv ├── benchmarks │ ├── README.md │ ├── curie_parsing │ │ ├── README.md │ │ ├── data.tsv │ │ └── results.svg │ ├── curie_validation │ │ ├── README.md │ │ ├── data.tsv │ │ └── results.svg │ └── uri_parsing │ │ ├── README.md │ │ ├── data.tsv │ │ └── results.svg ├── collections │ ├── README.md │ ├── collections.tsv │ └── collections.yml ├── contexts │ ├── README.md │ ├── bioregistry.context.jsonld │ ├── bioregistry.context.ttl │ ├── bioregistry.epm.json │ ├── bioregistry.rpm.json │ ├── obo.context.jsonld │ ├── obo.context.ttl │ ├── obo.epm.json │ ├── obo_synonyms.context.jsonld │ ├── obo_synonyms.context.ttl │ ├── semweb.context.jsonld │ ├── semweb.context.ttl │ ├── spar.context.jsonld │ └── spar.context.ttl ├── metaregistry │ ├── README.md │ ├── metaregistry.tsv │ └── metaregistry.yml ├── raw │ ├── aberowl.json │ ├── agroportal.json │ ├── biocontext.json │ ├── biolink.yaml │ ├── bioportal.json │ ├── cellosaurus.txt │ ├── cropoct.yaml │ ├── ecoportal.json │ ├── go.yml │ ├── miriam.json │ ├── n2t.yml │ ├── ncbi.html │ ├── obofoundry.yaml │ ├── ols.json │ ├── ontobee.html │ ├── prefixcommons.tsv │ ├── rrid.tsv │ ├── tib.json │ └── uniprot.json ├── rdf │ ├── README.md │ ├── bioregistry.jsonld │ ├── bioregistry.nt │ ├── bioregistry.ttl │ ├── schema.jsonld │ ├── schema.nt │ ├── schema.pdf │ ├── schema.svg │ └── schema.ttl ├── registry │ ├── README.md │ ├── publications.tsv │ ├── registry.json │ ├── registry.tsv │ └── registry.yml ├── sssom │ ├── README.md │ ├── bioregistry.sssom.tsv │ └── bioregistry.sssom.yml └── tables │ ├── comparison_goveranance.tex │ ├── comparison_goveranance.tsv │ ├── comparison_metadata.tex │ ├── comparison_metadata.tsv │ └── summary.tex ├── notebooks ├── Bioregistry Taxonomy Curation via Wikidata.ipynb └── Preparing the GO Annotation Database for Integration.ipynb ├── pyproject.toml ├── src └── bioregistry │ ├── __init__.py │ ├── __main__.py │ ├── analysis │ ├── __init__.py │ ├── bioregistry_diff.py │ ├── mapping_checking.py │ └── paper_ranking.py │ ├── app │ ├── __init__.py │ ├── api.py │ ├── cli.py │ ├── constants.py │ ├── impl.py │ ├── proxies.py │ ├── static │ │ ├── czi.svg │ │ ├── dalia.png │ │ ├── dfg.svg │ │ ├── funding-manifest-urls.txt │ │ ├── logo.svg │ │ ├── nfdi4chem.svg │ │ ├── northeastern.svg │ │ └── rwth-iac.svg │ ├── templates │ │ ├── base.html │ │ ├── collection.html │ │ ├── collections.html │ │ ├── context.html │ │ ├── contexts.html │ │ ├── contributor.html │ │ ├── contributors.html │ │ ├── highlights │ │ │ ├── owners.html │ │ │ ├── relations.html │ │ │ └── twitter.html │ │ ├── home.html │ │ ├── keyword.html │ │ ├── keywords.html │ │ ├── macros.html │ │ ├── meta │ │ │ ├── access.html │ │ │ ├── acknowledgements.html │ │ │ ├── download.html │ │ │ ├── related.html │ │ │ ├── schema.html │ │ │ ├── summary.html │ │ │ └── sustainability.html │ │ ├── metaresource.html │ │ ├── metaresources.html │ │ ├── prose.html │ │ ├── reference.html │ │ ├── resolve_errors │ │ │ ├── disallowed_identifier.html │ │ │ ├── invalid_identifier.html │ │ │ ├── missing_prefix.html │ │ │ └── missing_providers.html │ │ ├── resource.html │ │ └── resources.html │ ├── test.py │ ├── ui.py │ ├── utils.py │ └── wsgi.py │ ├── benchmarks │ ├── __init__.py │ ├── __main__.py │ ├── cli.py │ ├── curie_parsing.py │ ├── curie_validation.py │ └── uri_parsing.py │ ├── bibliometrics.py │ ├── cli.py │ ├── collection_api.py │ ├── compare.py │ ├── constants.py │ ├── curation │ ├── __init__.py │ ├── add_cessda.py │ ├── add_co_providers.py │ ├── add_descriptions_from_gs.py │ ├── add_examples.py │ ├── add_examples_from_ols.py │ ├── add_ontology_regexes.py │ ├── add_provider_status_curations.py │ ├── add_sweet.py │ ├── add_wikidata_database.py │ ├── bulk_import.py │ ├── clean_licenses.py │ ├── clean_name_suffixes.py │ ├── clean_publications.py │ ├── cleanup_authors.py │ ├── deprecation_diff.py │ ├── enrich_publications.py │ ├── find_contact_groups.py │ ├── fix_obo_purls.py │ ├── import_pc_semiautomatic.py │ ├── ingest_prefixmaps_bioportal.py │ ├── literature.py │ ├── make_description_curation_sheet.py │ ├── make_health_report_curation_sheet.py │ ├── map_bartoc_via_wikidata.py │ ├── map_re3data_via_fairsharing.py │ ├── nfdi_collections.py │ ├── odk_usage.py │ ├── rename_metaprefix.py │ ├── review_pc.py │ ├── seed_collection.py │ ├── suggest_author_curation.py │ └── suggest_uniprot_providers.py │ ├── data │ ├── README.md │ ├── __init__.py │ ├── bioregistry.json │ ├── collections.json │ ├── contexts.json │ ├── curated_mappings.sssom.tsv │ ├── curated_papers.tsv │ └── metaregistry.json │ ├── export │ ├── __init__.py │ ├── __main__.py │ ├── cli.py │ ├── prefix_maps.py │ ├── prefixcc.py │ ├── rdf_export.py │ ├── schema_export.py │ ├── sssom_export.py │ ├── tables_export.py │ ├── tsv_export.py │ ├── warnings_export.py │ └── yaml_export.py │ ├── external │ ├── __init__.py │ ├── aberowl │ │ ├── __init__.py │ │ └── processed.json │ ├── align.py │ ├── alignment_utils.py │ ├── bartoc │ │ ├── __init__.py │ │ └── processed.json │ ├── biocontext │ │ ├── __init__.py │ │ └── processed.json │ ├── biolink │ │ ├── __init__.py │ │ ├── processed.json │ │ └── processing_biolink.json │ ├── bioportal │ │ ├── __init__.py │ │ ├── agroportal.json │ │ ├── agroportal.py │ │ ├── bioportal.json │ │ ├── bioportal.py │ │ ├── ecoportal.json │ │ └── ecoportal.py │ ├── cellosaurus │ │ ├── __init__.py │ │ └── processed.json │ ├── cheminf │ │ ├── __init__.py │ │ └── processed.json │ ├── cropoct │ │ ├── __init__.py │ │ └── processed.json │ ├── edam │ │ ├── __init__.py │ │ └── processed.json │ ├── fairsharing │ │ ├── __init__.py │ │ └── processed.json │ ├── go │ │ ├── __init__.py │ │ ├── processed.json │ │ └── processing_go.json │ ├── hl7 │ │ ├── OID_Report.csv │ │ └── __init__.py │ ├── integbio │ │ ├── __init__.py │ │ └── processed.json │ ├── lov │ │ ├── __init__.py │ │ └── processed.json │ ├── miriam │ │ ├── __init__.py │ │ └── processed.json │ ├── n2t │ │ ├── __init__.py │ │ └── processed.json │ ├── ncbi │ │ ├── __init__.py │ │ └── processed.json │ ├── obofoundry │ │ ├── __init__.py │ │ └── processed.json │ ├── ols │ │ ├── __init__.py │ │ ├── processed.json │ │ ├── processing_ols.json │ │ ├── tib-processed.json │ │ ├── tib-processing-config.json │ │ └── tib.py │ ├── ontobee │ │ ├── __init__.py │ │ └── processed.json │ ├── pathguide │ │ └── __init__.py │ ├── prefixcommons │ │ ├── __init__.py │ │ └── processed.json │ ├── re3data │ │ ├── __init__.py │ │ └── processed.json │ ├── rrid │ │ └── __init__.py │ ├── togoid │ │ ├── __init__.py │ │ └── processed.json │ ├── uniprot │ │ ├── __init__.py │ │ └── processed.json │ ├── wikidata │ │ ├── __init__.py │ │ └── processed.json │ └── zazuko │ │ ├── __init__.py │ │ └── processed.json │ ├── gh │ ├── __init__.py │ ├── github_client.py │ └── new_prefix.py │ ├── health │ ├── __init__.py │ ├── __main__.py │ ├── check_homepages.py │ ├── check_providers.py │ └── cli.py │ ├── license_standardizer.py │ ├── lint.py │ ├── metaresource_api.py │ ├── pandas.py │ ├── parse_iri.py │ ├── parse_version_iri.py │ ├── py.typed │ ├── record_accumulator.py │ ├── reference.py │ ├── resolve.py │ ├── resolve_identifier.py │ ├── resource_manager.py │ ├── schema │ ├── __init__.py │ ├── constants.py │ ├── schema.json │ ├── struct.py │ └── utils.py │ ├── schema_utils.py │ ├── summary.py │ ├── upload_ndex.py │ ├── uri_format.py │ ├── utils.py │ ├── validate │ ├── __init__.py │ ├── cli.py │ └── utils.py │ └── version.py ├── tests ├── __init__.py ├── resources │ ├── ncbiortholog_test.json │ └── vibso_test.json ├── test_acquisition.py ├── test_api.py ├── test_collections.py ├── test_contexts.py ├── test_curated_mappings.py ├── test_curated_papers.py ├── test_data.py ├── test_data_slow.py ├── test_duplicates.py ├── test_identifiers_org.py ├── test_indra.py ├── test_manager.py ├── test_metaregistry.py ├── test_new_prefix.py ├── test_obofoundry.py ├── test_ols.py ├── test_pandas.py ├── test_paper_ranking.py ├── test_reference.py ├── test_resolve.py ├── test_sparql.py ├── test_usages.py ├── test_utils.py ├── test_validation.py └── test_web │ ├── __init__.py │ ├── test_api.py │ └── test_ui.py └── tox.ini /.github/ISSUE_TEMPLATE/add-collection-prefix.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/biopragmatics/bioregistry/HEAD/.github/ISSUE_TEMPLATE/add-collection-prefix.yml -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/add-new-collection.md: -------------------------------------------------------------------------------- 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