{% extends "prose.html" %} {% block title %}Related{% endblock %} {% macro render_circle(value, link=None) -%} {% if link %} {{ schema_status_map[value] }} {% else %} {{ schema_status_map[value] }} {% endif %} {% endmacro %} {% macro registry_field_dl(cls, key) -%} {% if is_pydantic_1 %} {% set field = cls.__fields__[key].field_info %}
An overview on registries covering biomedical ontologies, controlled vocabularies, and databases.
A {{ schema_status_map[True] }} means the field is required. A {{ schema_status_map["present"] }} means it is part of the schema, but not required or incomplete on some entries. A {{ schema_status_map[False] }} means that it is not part of the metadata schema. For lookup services like the OLS, some fields (i.e., Example ID, Default Provider, Alternate Providers) are omitted because inclusion would be redundant.
Registry | Data Model Score | Name | Homepage | Description | Example | Pattern | Provider | Alternate Providers | Alternate Prefixes | License | Version | Contact |
---|---|---|---|---|---|---|---|---|---|---|---|---|
{{ registry.get_short_name() }} | {{ registry.availability.score() }} | {{ render_circle(registry.availability.name) }} | {{ render_circle(registry.availability.homepage) }} | {{ render_circle(registry.availability.description) }} | {{ render_circle(registry.availability.example) }} | {{ render_circle(registry.availability.pattern) }} | {{ render_circle(registry.availability.provider) }} | {{ render_circle(registry.availability.alternate_providers) }} | {{ render_circle(registry.availability.synonyms) }} | {{ render_circle(registry.availability.license) }} | {{ render_circle(registry.availability.version) }} | {{ render_circle(registry.availability.contact) }} |
Notes: Several of Wikidata's fields can be accessed indirectly with alternative SPARQL queries. Non-english language registries in the OntoPortal Alliance were not considered.
This section provides a systematic evaluation and comparison of the capabilities of each registry.
Registry | Mappings | Quality Score | Structured Data | Bulk Data | Requires Authentication | Automatable Download | Permissive License | Prefix Search | Prefix Provider | CURIE Resolver | CURIE Lookup |
---|---|---|---|---|---|---|---|---|---|---|---|
{{ registry.get_short_name() }} | {{ mapping_counts[registry.prefix] }} | {{ registry.get_quality_score() }} | {{ render_circle(registry.qualities.structured_data) }} | {{ render_circle(registry.qualities.bulk_data) }} | {{ render_circle(registry.qualities.no_authentication) }} | {{ render_circle(registry.qualities.automatable_download) }} | {{ render_circle(registry.has_permissive_license) }} | {{ render_circle(registry.availability.search) }} | {{ render_circle(registry.is_prefix_provider) }} | {{ render_circle(registry.is_resolver) }} | {{ render_circle(registry.is_lookup) }} |
This section provides a systematic evaluation and comparison of the governance and standard operating procedures for each registry. We generated the following list of objective, measurable metrics:
We have made a survey of a subset of these questions which are presented in the table below, but, first, an explanation of each field is given.
Registry | Score | Accepts External Contributions | Public Version-Controlled Data | Issue Tracker | Review Team | Scope | Status |
---|---|---|---|---|---|---|---|
{{ registry.get_short_name() }} | {{ registry.governance.score() }} | {{ render_circle(registry.governance.accepts_external_contributions) }} | {{ render_circle(registry.governance.public_version_controlled_data, registry.governance.data_repository) }} | {% if registry.governance.issue_tracker %} {% endif %} | {{ registry.governance.review_team }} | {{ registry.governance.scope }} | {{ registry.governance.status }} |
The semantic web and ontology communities are bound to the use of IRIs as identifiers and therefore are very interested in the interconversion between compact identifiers (i.e., CURIEs) and IRIs. While the Bioregistry provides many tools for one way conversion from CURIEs to IRIs, there are several related packages that help parse CURIEs from IRIs: