{% extends "prose.html" %} {% block title %}Related{% endblock %} {% macro render_circle(value) -%} {{ schema_status_map[value] }} {% endmacro %} {% macro registry_field_dl(cls, key) -%} {% set field = cls.__fields__[key].field_info %}
{{ field.title or key.replace("_", " ").title() }}
{{ field.description }}
{% endmacro %} {% block styles %} {{ super() }} {% endblock %} {% block scripts %} {{ super() }} {% endblock %} {% block content %}

Comparison of Registries

An overview on registries covering biomedical ontologies, controlled vocabularies, and databases.

Data Models

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.

Caveats: Several of Wikidata's fields can be accessed indirectly with alternative SPARQL queries. BioPortal's data is locked behind an API that requires a key and has rate limited access. The Crop Ontology Curation Tool does not list homepages because it is the homepage itself. Non-english language registries in the OntoPortal Alliance were not included.

{% for registry in registries %} {% endfor %}
Registry Score Name Homepage Description Example Pattern Provider Alternate Providers Alternate Prefixes License Version Contact
{{ registry.get_short_name() }} {{ registry.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) }}

Capabilities

This section provides a systematic evaluation and comparison of the capabilities of each registry.

{{ registry_field_dl(registry_schema_cls, "fair") }} {{ registry_field_dl(registry_schema_cls, "search") }}
Provider
The registry provides information about its own prefixes either in the form of a web page or an API endpoint. These can be accessed through a stable URL into wich a prefix can be formatted.
Resolver
The registry can act as a resolver, i.e., it redirects to an external page about a given biomedical concept or entity based on its CURIE and the registry's internal metadata data about the prefix's associated URI format string.
Lookup
The registry can act as a lookup service, i.e., it gives information about a given biomedical concept or entity based on its CURIE.
{% for registry in registries %} {% endfor %}
Registry Mappings FAIR Search Provider Resolver Lookup
{{ registry.get_short_name() }} {{ mapping_counts[registry.prefix] }} {{ render_circle(registry.availability.fair) }} {{ render_circle(registry.availability.search) }} {{ render_circle(registry.provider_uri_format is not none) }} {{ render_circle(registry.is_resolver) }} {{ render_circle(registry.is_lookup) }}

Governance

This section provides a systematic evaluation and comparison of the governance and standard operating procedures for each registry.

{{ registry_field_dl(registry_governance_cls, "accepts_external_contributions") }} {{ registry_field_dl(registry_governance_cls, "public_version_control") }} {{ registry_field_dl(registry_governance_cls, "review_team") }} {{ registry_field_dl(registry_governance_cls, "scope") }} {{ registry_field_dl(registry_governance_cls, "status") }}
{% for registry in registries %} {% endfor %}
Registry Accepts External Contributions Public Version Control Review Team Scope Status
{{ registry.get_short_name() }} {{ render_circle(registry.governance.accepts_external_contributions) }} {{ render_circle(registry.governance.public_version_control) }} {{ registry.governance.review_team }} {{ registry.governance.scope }} {{ registry.governance.status }}

Related Software

Conversion between CURIEs and IRIs

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:

{% endblock %}