bioregistry 0.13.10__tar.gz → 0.13.12__tar.gz

{bioregistry-0.13.10 → bioregistry-0.13.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.10
+Version: 0.13.12
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.10 → bioregistry-0.13.12}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.10"
+version = "0.13.12"
 description = "Integrated registry of biological databases and nomenclatures"
 readme = "README.md"
 authors = [
@@ -254,7 +254,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.13.10"
+current_version = "0.13.12"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{bioregistry-0.13.10 → bioregistry-0.13.12}/src/bioregistry/__init__.py

@@ -131,6 +131,7 @@ from .schema import (
     Author,
     Collection,
     Context,
+    Organization,
     Provider,
     Registry,
     Resource,
@@ -164,6 +165,7 @@ __all__ = [
     "NormalizedNamableReference",
     "NormalizedNamedReference",
     "NormalizedReference",
+    "Organization",
     "Provider",
     "Registry",
     "Resource",

{bioregistry-0.13.10 → bioregistry-0.13.12}/src/bioregistry/app/templates/base.html

@@ -37,6 +37,12 @@
                     padding-bottom: 2em;
                     background-color: #f5f5f5;
                 }
+                dl {
+                    margin-bottom: 0;
+                }
+                dl dd:last-child {
+                    margin-bottom: 0;
+                }
             </style>
         {% endblock %}
 

{bioregistry-0.13.10 → bioregistry-0.13.12}/src/bioregistry/app/templates/collection.html

@@ -42,14 +42,21 @@
                 <dt>Identifier</dt>
                 <dd><code>{{ identifier }}</code></dd>
                 <dt>Contributors</dt>
-                <dd>
-                    {% for author in entry.authors %}
+                    {%- for author in entry.authors %}
+                    <dd style="margin-bottom: 0;">
                         <a href="{{ url_for("metaregistry_ui.contributor", orcid=author.orcid) }}">
                             {{ author.name }}
                             <i class="fab fa-orcid"></i>
-                        </a>{% if not loop.last %}, {% endif %}
-                    {% endfor %}
-                </dd>
+                        </a>
+                    </dd>
+                    {%- endfor %}
+                    {%- if entry.organizations %}
+                    {%- for organization in entry.organizations %}
+                    <dd style="margin-bottom: 0;">
+                        <a href="{{ organization.link }}">{{ organization.name }}</a>
+                    </dd>
+                    {%- endfor %}
+                    {%- endif %}
                 <dt>Size</dt>
                 <dd>{{ entry.resources | length }}</dd>
                 {% if entry.references %}
@@ -60,7 +67,7 @@
                 {% endif %}
             </dl>
         </div>
-        <table class="table table-striped">
+        <table class="table table-striped" style="margin-bottom: 0;">
             <thead>
             <tr>
                 <th scope="col">Prefix</th>

bioregistry-0.13.12/src/bioregistry/app/templates/resource-bibliometrics.html

@@ -0,0 +1,79 @@
+<div class="card" style="margin-top: 20px">
+    <h5 class="card-header">Contacts</h5>
+    <div class="card-body">
+        {%- if resource.contact_group_email %}
+        <a class="badge badge-pill badge-light" href="{{ resource.contact_group_email }}">
+            Mailing List <i class="fas fa-address-book"></i></i></a>
+        {%- endif %}
+        {%- if resource.contact_page %}
+        <a class="badge badge-pill badge-light" href="{{ resource.contact_page }}">
+            Contact Page <i class="fas fa-address-book"></i></i></a>
+        {%- endif %}
+        <dl>
+            <dt>
+                Contact
+                {% if contact %}
+                <a type="button" data-toggle="modal" data-target="#contact-modal">
+                    <i class="far fa-question-circle"></i>
+                </a>
+                {% endif %}
+            </dt>
+            <dd>
+                {% if contact %}
+                {{ utils.render_author(contact, link=none) }}
+                {% else %}
+                <span class="badge badge-pill badge-warning">Missing Contact</span>
+                {% endif %}
+            </dd>
+            {%- for secondary_contact in resource.contact_extras or [] %}
+            <dd>
+                {{ utils.render_author(secondary_contact, link=none) }}
+            </dd>
+            {%- endfor %}
+
+            {% if resource.owners %}
+            <dt>Identifier Space Owner{% if resource.owners | length > 1 %}s{% endif %}</dt>
+            {% for owner in resource.owners %}
+            <dd>
+                <a href="{{ owner.link }}">{{ owner.name }}</a>
+                {% if owner.partnered %}
+                <a href="{{ config.METAREGISTRY_REPOSITORY }}/blob/main/docs/GOVERNANCE.md#partners"
+                   class="badge badge-pill badge-info" data-toggle="tooltip"
+                   title="This organization has partnered with the {{ config.METAREGISTRY_TITLE }} to proactively maintain this record. Click to see related project governance.">
+                    Partnered
+                </a>
+                {% endif %}
+            </dd>
+            {% endfor %}
+            {% endif %}
+            {% if resource.contributor or resource.contributor_extras %}
+            <dt>Contributors</dt>
+            {% if resource.contributor %}
+            <dd>
+                <span class="badge badge-info">submitter</span> {{ utils.render_author(resource.contributor,
+                link=url_for('metaregistry_ui.contributor', orcid=resource.contributor.orcid)) }}
+            </dd>
+            {% endif %}
+            {% for contributor in resource.contributor_extras or [] %}
+            <dd>
+                <span class="badge badge-info">contributor</span> {{ utils.render_author(contributor,
+                link=url_for('metaregistry_ui.contributor', orcid=contributor.orcid)) }}
+            </dd>
+            {% endfor %}
+            {% endif %}
+
+            {% if resource.reviewer %}
+            <dt>Reviewer</dt>
+            <dd>
+                {{ utils.render_author(resource.reviewer, link=url_for('metaregistry_ui.contributor',
+                orcid=resource.reviewer.orcid)) }}
+            </dd>
+            {%- for reviewer in resource.reviewer_extras or [] %}
+            <dd>
+                {{ utils.render_author(reviewer, link=url_for('metaregistry_ui.contributor', orcid=reviewer.orcid)) }}
+            </dd>
+            {%- endfor %}
+            {% endif %}
+        </dl>
+    </div>
+</div>

bioregistry-0.13.12/src/bioregistry/app/templates/resource-standards.html

@@ -0,0 +1,89 @@
+<div class="card" style="margin-top: 20px">
+    <h5 class="card-header">Identifier Standards</h5>
+    <div class="card-body">
+        <dl>
+            <dt>Pattern for Local Unique Identifiers</dt>
+            <dd>
+                {% if pattern %}
+                <p>
+                    Local identifiers in {{ name_pack.value }} should match this
+                    regular expression:<br/><kbd>{{ pattern }}</kbd>
+                </p>
+                {% elif has_no_terms %}
+                <span class="badge badge-pill badge-secondary">No terms in {{ prefix }}</span>
+                {% else %}
+                <span class="badge badge-pill badge-warning">Missing LUI pattern</span>
+                {% endif %}
+            </dd>
+            <dt>Example Local Unique Identifier{% if resource.example_extras %}s{% endif %}</dt>
+            <dd>
+                {% if example %}
+                <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=example) }}">{{ example
+                }}</a>
+                {% if providers %}
+                &nbsp;
+                <a class="badge badge-pill badge-info" href="{{ url_for("metaregistry_ui.resolve", prefix=prefix,
+                identifier=example) }}"><i class="fas fa-share-square"></i> Resolve</a>
+                {% endif %}
+                {% for extra_example in example_extras %}
+                <br/>
+                <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=extra_example) }}">{{
+                extra_example }}</a>
+                {% if providers %}
+                &nbsp;
+                <a class="badge badge-pill badge-info" href="{{ url_for("metaregistry_ui.resolve", prefix=prefix,
+                identifier=extra_example) }}"><i class="fas fa-share-square"></i> Resolve</a>
+                {% endif %}
+                {% endfor %}
+                {% elif has_no_terms %}
+                <span class="badge badge-pill badge-secondary">No Terms in {{ prefix }}</span>
+                {% else %}
+                <span class="badge badge-pill badge-warning">Missing Example Local Unique Identifier</span>
+                {% endif %}
+            </dd>
+            {% if pattern and curie_pattern %}
+            <dt>Pattern for CURIES</dt>
+            <dd>
+                <p>
+                    Compact URIs (CURIEs) constructed from {{ name_pack.value }} should match
+                    this regular expression:<br/><kbd>{{ curie_pattern }}</kbd>
+                </p>
+            </dd>
+            {% endif %}
+            {% if example and example_curie %}
+            <dt>Example CURIE{% if resource.example_extras %}s{% endif %}</dt>
+            <dd>
+                <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=example) }}">{{
+                example_curie }}</a>
+                {% for example_curie_extra, example_extra in zip(example_curie_extras, example_extras) %}
+                <br/>
+                <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=example_extra) }}">{{
+                example_curie_extra }}</a>
+                {% endfor %}
+            </dd>
+            {% endif %}
+            {% if resource.get_rdf_uri_format() %}
+            <dt>Pattern for RDF URIs</dt>
+            <dd><kbd>{{ resource.get_rdf_uri_format() }}</kbd></dd>
+            <dt>Example RDF URI</dt>
+            {% set rdf_uri_example = resource.get_rdf_uri_format().replace("$1", example) %}
+            <dd><a href="{{ rdf_uri_example }}">{{ rdf_uri_example }}</a></dd>
+            {% endif %}
+            {% if namespace_in_lui %}
+            <dt><i class="fas fa-info-circle"></i> MIRIAM Namespace Embedded in LUI</dt>
+            <dd>
+                The legacy MIRIAM standard for generating CURIEs with this resource
+                annotates the <code>namespaceEmbeddedInLUI</code> as true.
+                {{ get_banana_text() }}
+            </dd>
+            {% elif banana %}
+            <dt><i class="fas fa-info-circle"></i> Namespace Embedded in LUI</dt>
+            <dd>
+                This resource has been annotated by the {{ config.METAREGISTRY_TITLE }} as having a potential
+                namespace embedded in LUI.
+                {{ get_banana_text() }}
+            </dd>
+            {% endif %}
+        </dl>
+    </div>
+</div>

{bioregistry-0.13.10 → bioregistry-0.13.12}/src/bioregistry/app/templates/resource.html

@@ -189,14 +189,6 @@
                             Repository <i class="fab fa-github"></i>
                         </a>
                     {% endif %}
-                    {%- if resource.contact_group_email %}
-                        <a class="badge badge-pill badge-light" href="{{ resource.contact_group_email }}">
-                            Mailing List <i class="fas fa-address-book"></i></i></a>
-                    {%- endif %}
-                    {%- if resource.contact_page %}
-                        <a class="badge badge-pill badge-light" href="{{ resource.contact_page }}">
-                            Contact Page <i class="fas fa-address-book"></i></i></a>
-                    {%- endif %}
                     {% if obo_download %}
                         <a class="badge badge-pill badge-light" href="{{ obo_download }}">
                             OBO <i class="fas fa-download"></i>
@@ -238,173 +230,28 @@
                         </a>
                     {% endif %}
                 </dd>
-                <dt>
-                    Contact
-                    {% if contact %}
-                    <a type="button" data-toggle="modal" data-target="#contact-modal">
-                        <i class="far fa-question-circle"></i>
-                    </a>
-                    {% endif %}
-                </dt>
-                <dd>
-                    {% if contact %}
-                        {{ utils.render_author(contact, link=none) }}
-                    {% else %}
-                        <span class="badge badge-pill badge-warning">Missing Contact</span>
-                    {% endif %}
-                </dd>
-                {%- for secondary_contact in resource.contact_extras or [] %}
-                <dd>
-                    {{ utils.render_author(secondary_contact, link=none) }}
-                </dd>
-                {%- endfor %}
-                {% if resource.owners %}
-                    <dt>Identifier Space Owner{% if resource.owners | length > 1 %}s{% endif %}</dt>
-                    {% for owner in resource.owners %}
-                    <dd>
-                    <a href="{{ owner.link }}">{{ owner.name }}</a>
-                    {% if owner.partnered %}
-                    <a href="{{ config.METAREGISTRY_REPOSITORY }}/blob/main/docs/GOVERNANCE.md#partners"
-                           class="badge badge-pill badge-info" data-toggle="tooltip"
-                           title="This organization has partnered with the {{ config.METAREGISTRY_TITLE }} to proactively maintain this record. Click to see related project governance.">
-                        Partnered
-                    </a>
-                    {% endif %}
-                    </dd>
-                    {% endfor %}
-                {% endif %}
-                <dt>Pattern for Local Unique Identifiers</dt>
-                <dd>
-                    {% if pattern %}
-                        <p>
-                            Local identifiers in {{ name_pack.value }} should match this
-                            regular expression:<br/><kbd>{{ pattern }}</kbd>
-                        </p>
-                    {% elif has_no_terms %}
-                        <span class="badge badge-pill badge-secondary">No terms in {{ prefix }}</span>
-                    {% else %}
-                        <span class="badge badge-pill badge-warning">Missing LUI pattern</span>
-                    {% endif %}
-                </dd>
-                <dt>Example Local Unique Identifier{% if resource.example_extras %}s{% endif %}</dt>
-                <dd>
-                    {% if example %}
-                        <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=example) }}">{{ example }}</a>
-                        {% if providers %}
-                        &nbsp;
-                        <a class="badge badge-pill badge-info" href="{{ url_for("metaregistry_ui.resolve", prefix=prefix, identifier=example) }}"><i class="fas fa-share-square"></i> Resolve</a>
-                        {% endif %}
-                        {% for extra_example in example_extras %}
-                            <br />
-                            <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=extra_example) }}">{{ extra_example }}</a>
-                            {% if providers %}
-                                &nbsp;
-                                <a class="badge badge-pill badge-info" href="{{ url_for("metaregistry_ui.resolve", prefix=prefix, identifier=extra_example) }}"><i class="fas fa-share-square"></i> Resolve</a>
-                            {% endif %}
-                        {% endfor %}
-                    {% elif has_no_terms %}
-                        <span class="badge badge-pill badge-secondary">No Terms in {{ prefix }}</span>
-                    {% else %}
-                        <span class="badge badge-pill badge-warning">Missing Example Local Unique Identifier</span>
-                    {% endif %}
-                </dd>
-                {% if pattern and curie_pattern %}
-                <dt>Pattern for CURIES</dt>
-                <dd>
-                    <p>
-                        Compact URIs (CURIEs) constructed from {{ name_pack.value }} should match
-                        this regular expression:<br/><kbd>{{ curie_pattern }}</kbd>
-                    </p>
-                </dd>
-                {% endif %}
-                {% if example and example_curie %}
-                <dt>Example CURIE{% if resource.example_extras %}s{% endif %}</dt>
-                <dd>
-                    <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=example) }}">{{ example_curie }}</a>
-                    {% for example_curie_extra, example_extra in zip(example_curie_extras, example_extras) %}
-                        <br />
-                        <a href="{{ url_for("metaregistry_ui.reference", prefix=prefix, identifier=example_extra) }}">{{ example_curie_extra }}</a>
-                    {% endfor %}
-                </dd>
-                {% endif %}
-                {% if namespace_in_lui %}
-                    <dt><i class="fas fa-info-circle"></i> MIRIAM Namespace Embedded in LUI</dt>
-                    <dd>
-                        The legacy MIRIAM standard for generating CURIEs with this resource
-                        annotates the <code>namespaceEmbeddedInLUI</code> as true.
-                        {{ get_banana_text() }}
-                    </dd>
-                {% elif banana %}
-                    <dt><i class="fas fa-info-circle"></i> Namespace Embedded in LUI</dt>
-                    <dd>
-                        This resource has been annotated by the {{ config.METAREGISTRY_TITLE }} as having a potential
-                        namespace embedded in LUI.
-                        {{ get_banana_text() }}
-                    </dd>
-                {% endif %}
 
                 {% set publications = resource.get_publications() %}
                 {% if publications %}
                     <dt>Publications</dt>
-                    <dd>
-                        {% if publications | length == 1 %}
-                            {{ utils.render_publication(publications[0]) }}
-                        {% else %}
-                            <ul>
-                                {% for publication in publications %}
-                                    <li>{{ utils.render_publication(publication) }}</li>
-                                {% endfor %}
-                            </ul>
-                        {% endif %}
-                    </dd>
+                    {%- for publication in publications %}
+                    <dd>{{ utils.render_publication(publication) }}</dd>
+                    {%- endfor %}
                 {% endif %}
                 {% if resource.references %}
                     <dt>References</dt>
-                    <dd>
-                        {% if resource.references | length == 1 %}
-                            {{ utils.render_reference(resource.references[0]) }}
-                        {% else %}
-                            <ul>
-                                {% for reference in resource.references %}
-                                    <li>{{ utils.render_reference(reference) }}</li>
-                                {% endfor %}
-                            </ul>
-                        {% endif %}
-                    </dd>
-                {% endif %}
-                {% if resource.contributor or resource.contributor_extras %}
-                    <dt>Contributors</dt>
-                    <dd>
-                        <ul>
-                            {% if resource.contributor %}
-                                <li>
-                                    <span class="badge badge-info">submitter</span> {{ utils.render_author(resource.contributor, link=url_for('metaregistry_ui.contributor', orcid=resource.contributor.orcid)) }}
-                                </li>
-                            {% endif %}
-                            {% for contributor in resource.contributor_extras or [] %}
-                                <li>
-                                    <span class="badge badge-info">contributor</span> {{ utils.render_author(contributor, link=url_for('metaregistry_ui.contributor', orcid=contributor.orcid)) }}
-                                </li>
-                            {% endfor %}
-                        </ul>
-                    </dd>
-                {% endif %}
-                {% if resource.reviewer %}
-                    <dt>Reviewer</dt>
-                    <dd>
-                        {{ utils.render_author(resource.reviewer, link=url_for('metaregistry_ui.contributor', orcid=resource.reviewer.orcid)) }}
-                    </dd>
-                    {%- for reviewer in resource.reviewer_extras or [] %}
-                    <dd>
-                        {{ utils.render_author(reviewer, link=url_for('metaregistry_ui.contributor', orcid=reviewer.orcid)) }}
-                    </dd>
+                    {%- for reference in resource.references %}
+                    <dd>{{ utils.render_reference(reference) }}</dd>
                     {%- endfor %}
                 {% endif %}
             </dl>
         </div>
-
     </div>
 
+    {% include "resource-standards.html" %}
+
+    {% include "resource-bibliometrics.html" %}
+
     {% if provides or provided_by or part_of or has_parts or has_canonical or canonical_for or depends_on or appears_in or in_collections %}
     <div class="card" style="margin-top: 20px">
         <a id="ontology"></a>
@@ -572,20 +419,6 @@
         </div>
     {% endif %}
 
-    {% if resource.get_rdf_uri_format() %}
-        <div class="card" style="margin-top: 20px">
-            <h5 class="card-header">RDF Information</h5>
-            <div class="card-body">
-                <p>
-                    When using this resource in RDF, the following URI format should be used:
-                </p>
-                <p>
-                    <code>{{ resource.get_rdf_uri_format() }}</code>
-                </p>
-            </div>
-        </div>
-    {% endif %}
-
     {% if not resource.no_own_terms %}
         <div class="card" style="margin-top: 20px">
             <a id="providers"></a>
@@ -623,7 +456,7 @@
                 {% if providers %}
                 <p>
                     The local unique identifier <code>{{ example }}</code> is used to demonstrate the providers
-                    available for {{ name_pack.value }}. Some providers may use a different example, which is displayed in the table below. 
+                    available for {{ name_pack.value }}. Some providers may use a different example, which is displayed in the table below.
                     A guide for curating additional providers can be found
                     <a href="{{ config.METAREGISTRY_REPOSITORY_PAGES }}/curation/providers">here</a>.
                 </p>

bioregistry-0.13.12/src/bioregistry/curation/add_linkml.py

@@ -0,0 +1,89 @@
+"""Import a resource from a LinkML configuration.
+
+This curation workflow can be called from the command line by passing a URL to a LinkML
+YAML configuration file like in the following:
+
+.. code-block:: console
+
+    $ python -m bioregistry.curation.add_linkml https://github.com/HendrikBorgelt/CatCore/blob/main/src/catcore/schema/catcore.yaml
+
+Here are some more example LinkML YAML configuration files:
+
+- https://github.com/HendrikBorgelt/CatCore/blob/main/src/catcore/schema/catcore.yaml
+- https://github.com/mapping-commons/sssom/blob/master/src/sssom_schema/schema/sssom_schema.yaml
+
+.. warning::
+
+    This workflow doesn't produce complete Bioregistry records! You still must add:
+
+    1. ``homepage``
+    2. ``contributor``
+
+    Given most LinkML configurations are on GitHub, you can probably figure out:
+
+    - ``repository``
+    - ``contact``
+"""
+
+import click
+import requests
+import yaml
+
+import bioregistry
+
+__all__ = [
+    "get_resource_from_linkml",
+    "import_from_linkml",
+    "import_from_linkml_cli",
+]
+
+
+def import_from_linkml(url: str) -> None:
+    """Get a resource from a LinkML configuration and write it to the registry.
+
+    :param url: The URL to a LinkML YAML configuration file.
+    :returns: A Bioregistry resource object
+    """
+    resource = get_resource_from_linkml(url)
+    bioregistry.manager.add_resource(resource)
+    bioregistry.manager.write_registry()
+
+
+def get_resource_from_linkml(url: str) -> bioregistry.Resource:
+    """Get a resource from a LinkML configuration.
+
+    :param url: The URL to a LinkML YAML configuration file.
+    :returns: A Bioregistry resource object
+    """
+    res = requests.get(url, timeout=5)
+    res.raise_for_status()
+    data = yaml.safe_load(res.text)
+
+    prefix = data.pop("default_prefix")
+    prefix_map = data.pop("prefixes")
+    uri_prefix = prefix_map.pop(prefix)
+
+    classes = data.pop("classes")
+    first_class = next(iter(classes))
+
+    rv = bioregistry.Resource(
+        prefix=prefix,
+        name=data.pop("title"),
+        description=data.pop("description").replace("\n", " ").replace("  ", " "),
+        license=data.pop("license", None),
+        uri_format=f"{uri_prefix}$1",
+        example=first_class,
+        version=data.pop("version", None),
+    )
+    return rv
+
+
+@click.command()
+@click.argument("url")
+def import_from_linkml_cli(url: str) -> None:
+    """Add a resource from the URL."""
+    import_from_linkml(url)
+
+
+if __name__ == "__main__":
+    import_from_linkml_cli()

bioregistry-0.13.12/src/bioregistry/curation/add_nfdi_section_collections.py

@@ -0,0 +1,60 @@
+"""Summarize NFDI consortia that don't have a collection."""
+
+import click
+import wikidata_client
+
+import bioregistry
+from bioregistry import Author, Collection, Organization
+
+SPARQL = """\
+SELECT ?wikidata ?name ?ror
+WHERE {
+    ?wikidata wdt:P361 wd:Q61658497; wdt:P31 wd:Q98270496 ; rdfs:label ?name .
+    FILTER (LANG(?name) = 'en')
+    OPTIONAL { ?wikidata wdt:P6782 ?ror . }
+}
+"""
+
+
+@click.command()
+def main() -> None:
+    """Summarize NFDI consortia that don't have a collection."""
+    collections = bioregistry.read_collections()
+    max_collection_id = max(map(int, collections))
+
+    wikidata_client.query(SPARQL)
+
+    nfdi_organizations = [
+        Organization.model_validate(record) for record in wikidata_client.query(SPARQL)
+    ]
+    wikidata_to_organization: dict[str, Organization] = {
+        organization.wikidata: organization
+        for organization in nfdi_organizations
+        if organization.wikidata
+    }
+    covered_wikidata: set[str] = {
+        organization.wikidata
+        for collection in collections.values()
+        for organization in collection.organizations or []
+        if organization.wikidata
+    }
+    missing = set(wikidata_to_organization) - covered_wikidata
+    if missing:
+        nfdi = Organization(name="NFDI", wikidata="Q61658497", ror="05qj6w324")
+        for wikidata in sorted(missing):
+            organization = wikidata_to_organization[wikidata]
+            max_collection_id += 1
+            collection = Collection(
+                identifier=f"{max_collection_id:07}",
+                name=f"{organization.name} Collection",
+                description=f"A collection of ontologies, controlled vocabularies, database, and schemas relevant for {organization.name}",
+                resources=["bioregistry"],
+                authors=[Author.get_charlie()],
+                organizations=[organization, nfdi],
+            )
+            bioregistry.manager.add_collection(collection)
+        bioregistry.manager.write_collections()
+
+
+if __name__ == "__main__":
+    main()