Propogate RDF URI format string to API and update EDAM

src/bioregistry/app/utils.py

@@ -35,6 +35,9 @@ def _get_resource_providers(
             metaprefix = prefix
             name = manager.get_name(prefix)
             homepage = manager.get_homepage(prefix)
+        elif metaprefix == "rdf":
+            name = f"{manager.get_name(prefix)} (RDF)"
+            homepage = manager.get_homepage(prefix)
         else:
             name = manager.get_registry_name(metaprefix)
             homepage = manager.get_registry_homepage(metaprefix)

src/bioregistry/data/bioregistry.json

@@ -27317,6 +27317,7 @@
       "prefix": "edam",
       "uri_format": "http://purl.bioontology.org/ontology/EDAM/$1"
     },
+    "name": "EDAM Ontology",
     "ols": {
       "contact": "[email protected]",
       "description": "EDAM is a simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use.",
@@ -27352,6 +27353,7 @@
         "year": 2013
       }
     ],
+    "rdf_uri_format": "http://edamontology.org/$1",
     "repository": "https://github.com/edamontology/edamontology",
     "twitter": "edamontology",
     "uri_format": "https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http://edamontology.org/$1"

src/bioregistry/resource_manager.py

@@ -1044,6 +1044,22 @@ def get_default_iri(self, prefix: str, identifier: str) -> Optional[str]:
             return None
         return entry.get_default_uri(identifier)
 
+    def get_rdf_uri(self, prefix: str, identifier: str) -> Optional[str]:
+        """Get the RDF URI for the given CURIE.
+
+        :param prefix: The prefix in the CURIE
+        :param identifier: The identifier in the CURIE
+        :return: A IRI string corresponding to the canonical RDF provider, if available.
+
+        >>> from bioregistry import manager
+        >>> manager.get_rdf_uri('edam', 'data_1153')
+        'http://edamontology.org/data_1153'
+        """
+        entry = self.get_resource(prefix)
+        if entry is None:
+            return None
+        return entry.get_rdf_uri(identifier)
+
     def get_miriam_curie(self, prefix: str, identifier: str) -> Optional[str]:
         """Get the identifiers.org CURIE for the given CURIE."""
         resource = self.get_resource(prefix)
@@ -1173,6 +1189,7 @@ def get_provider_functions(self) -> Mapping[str, Callable[[str, str], Optional[s
         """Return a mapping of provider functions."""
         return {
             "default": self.get_default_iri,
+            "rdf": self.get_rdf_uri,
             "miriam": self.get_miriam_iri,
             "obofoundry": self.get_obofoundry_iri,
             "ols": self.get_ols_iri,
@@ -1199,12 +1216,23 @@ def get_providers_list(self, prefix: str, identifier: str) -> Sequence[Tuple[str
             return rv
 
         bioregistry_link = self.get_bioregistry_iri(prefix, identifier)
-        if not bioregistry_link:
-            return rv
+        if bioregistry_link:
+            rv.append(("bioregistry", bioregistry_link))
+
+        def _key(t):
+            if t[0] == "default":
+                return 0
+            elif t[0] == "rdf":
+                return 1
+            elif t[0] == "bioregistry":
+                return 2
+            else:
+                return 3
 
-        # if a default URL is available, it goes first. otherwise the bioregistry URL goes first.
-        rv.insert(1 if rv[0][0] == "default" else 0, ("bioregistry", bioregistry_link))
+        rv = sorted(rv, key=_key)
         return rv
+        # if a default URL is available, it goes first. otherwise the bioregistry URL goes first.
+        # rv.insert(1 if rv[0][0] == "default" else 0, ("bioregistry", bioregistry_link))
 
     def get_providers(self, prefix: str, identifier: str) -> Dict[str, str]:
         """Get all providers for the CURIE.

src/bioregistry/schema/struct.py

@@ -685,6 +685,21 @@ def get_default_uri(self, identifier: str) -> Optional[str]:
             return None
         return fmt.replace("$1", identifier)
 
+    def get_rdf_uri(self, identifier: str) -> Optional[str]:
+        """Return the RDF URI for the identifier.
+
+        :param identifier: The local identifier in the nomenclature represented by this resource
+        :returns: The canonical RDF URI for the local identifier, if one can be constructed
+
+        >>> from bioregistry import get_resource
+        >>> get_resource("edam").get_rdf_uri("data_1153")
+        'http://edamontology.org/data_1153'
+        """
+        fmt = self.get_rdf_uri_format()
+        if fmt is None:
+            return None
+        return fmt.replace("$1", identifier)
+
     def __setitem__(self, key, value):  # noqa: D105
         setattr(self, key, value)