Add definition method to OLS implementation

Makefile

@@ -63,6 +63,8 @@ gendoc-itemlist: src/oaklib/datamodels/item_list.yaml
 	$(RUN_GENDOC)  $< -d docs/datamodels/item-list
 gendoc-ce: src/oaklib/datamodels/class_enrichment.yaml
 	$(RUN_GENDOC)  $< -d docs/datamodels/class-enrichment
+gendoc-vsc: src/oaklib/datamodels/value_set_configuration.yaml
+	$(RUN_GENDOC)  $< -d docs/datamodels/value-set-configuration
 
 nb:
 	$(RUN) jupyter notebook

src/oaklib/conf/lexmatch-rules-oboinowl-default.yaml

@@ -63,13 +63,13 @@ rules:
       weight: 2.0
 
   - synonymizer:
-      the_rule: Remove parentheses bound info from the label.
+      description: Remove parentheses bound info from the label.
       match: r'\([^)]*\)'
       match_scope: "*"
       replacement: ""
 
   - synonymizer:
-      the_rule: Remove box brackets bound info from the label.
+      description: Remove box brackets bound info from the label.
       match: r'\[[^)]*\]'
       match_scope: "*"
       replacement: ""

src/oaklib/datamodels/value_set_configuration.yaml

@@ -2,7 +2,7 @@ id: https://w3id.org/linkml/value-set-configuration
 title: Value Set Configuration
 name: value-set-configuration
 description: >-
-  A datamodel for configuring value sets and value set expabsions
+  A datamodel for configuring value sets and value set expansions
 license: https://creativecommons.org/publicdomain/zero/1.0/
 
 prefixes:
@@ -24,11 +24,12 @@ imports:
 #==================================
 classes:
   ValueSetConfiguration:
-    description: configuration for value sets
+    description: configuration for value set expansion
     attributes:
       default_resolver:
         range: Resolver
         inlined: true
+        description: The default resolver to use for value set expansion
       resource_resolvers:
         range: Resolver
         multivalued: true
@@ -37,6 +38,7 @@ classes:
         range: Resolver
         multivalued: true
         inlined: true
+        description: Mapping of prefixes to resolvers
 
   Resolver:
     description: A mechanism for resolving using an ontology
@@ -47,7 +49,7 @@ classes:
         description: The name of the resource or prefix
       shorthand_prefix:
       shorthand:
-        description: A shorthand for the resolver, using the OAK shorthand syntax
+        description: A shorthand for the resolver, using the OAK shorthand syntax, for example, 'obo:sqlite:cl'
       method:
         range: ResolverMethod
         description: >-

src/oaklib/implementations/ols/ols_implementation.py

@@ -1,6 +1,6 @@
 from collections import ChainMap
 from dataclasses import dataclass, field
-from typing import Any, ClassVar, Dict, Iterable, Iterator, List, Tuple, Union
+from typing import Any, ClassVar, Dict, Iterable, Iterator, List, Optional, Tuple, Union
 
 import requests
 from ols_client import Client, EBIClient, TIBClient
@@ -18,7 +18,7 @@
 from oaklib.interfaces.mapping_provider_interface import MappingProviderInterface
 from oaklib.interfaces.search_interface import SearchInterface
 from oaklib.interfaces.text_annotator_interface import TextAnnotatorInterface
-from oaklib.types import CURIE, PRED_CURIE
+from oaklib.types import CURIE, LANGUAGE_TAG, PRED_CURIE
 
 __all__ = [
     # Abstract classes
@@ -40,13 +40,14 @@
 
 
 @dataclass
-class BaseOlsImplementation(TextAnnotatorInterface, SearchInterface, MappingProviderInterface):
+class BaseOlsImplementation(MappingProviderInterface, TextAnnotatorInterface, SearchInterface):
     """
     Implementation over OLS and OxO APIs
     """
 
     ols_client_class: ClassVar[type[Client]]
     label_cache: Dict[CURIE, str] = field(default_factory=lambda: {})
+    definition_cache: Dict[CURIE, str] = field(default_factory=lambda: {})
     base_url = "https://www.ebi.ac.uk/spot/oxo/api/mappings"
     _prefix_map: Dict[str, str] = field(default_factory=lambda: {})
     focus_ontology: str = None
@@ -66,9 +67,84 @@ def add_prefix(self, curie: str, uri: str):
     def prefix_map(self) -> PREFIX_MAP:
         return ChainMap(super().prefix_map(), self._prefix_map)
 
-    def labels(self, curies: Iterable[CURIE]) -> Iterable[Tuple[CURIE, str]]:
+    def label(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
+        """
+        Fetch the label for a CURIE from OLS.
+
+        :param curie: The CURIE to fetch the label for
+        :param lang: Optional language tag (not currently supported by this implementation)
+        :return: The label for the CURIE, or None if not found
+        """
+        if curie in self.label_cache:
+            return self.label_cache[curie]
+
+        ontology = self.focus_ontology
+        iri = self.curie_to_uri(curie)
+        term = self.client.get_term(ontology=ontology, iri=iri)
+        if term and "label" in term:
+            self.label_cache[curie] = term["label"]
+            return term["label"]
+        return None
+
+    def labels(
+        self, curies: Iterable[CURIE], allow_none=True, lang: LANGUAGE_TAG = None
+    ) -> Iterable[Tuple[CURIE, str]]:
+        """
+        Fetch labels for multiple CURIEs.
+
+        :param curies: The CURIEs to fetch labels for
+        :param allow_none: Whether to include CURIEs with no label
+        :param lang: Optional language tag (not currently supported by this implementation)
+        :return: Iterator of (CURIE, label) tuples
+        """
+        for curie in curies:
+            label = self.label(curie, lang)
+            if label is None and not allow_none:
+                continue
+            yield curie, label
+
+    def definition(self, curie: CURIE, lang: Optional[LANGUAGE_TAG] = None) -> Optional[str]:
+        """
+        Fetch the definition for a CURIE from OLS.
+
+        :param curie: The CURIE to fetch the definition for
+        :param lang: Optional language tag (not currently supported by this implementation)
+        :return: The definition for the CURIE, or None if not found
+        """
+        if curie in self.definition_cache:
+            return self.definition_cache[curie]
+
+        ontology = self.focus_ontology
+        iri = self.curie_to_uri(curie)
+        term = self.client.get_term(ontology=ontology, iri=iri)
+        if term and "description" in term and term["description"]:
+            self.definition_cache[curie] = term["description"]
+            return term["description"]
+        return None
+
+    def definitions(
+        self,
+        curies: Iterable[CURIE],
+        include_metadata=False,
+        include_missing=False,
+        lang: Optional[LANGUAGE_TAG] = None,
+    ) -> Iterator[Tuple[CURIE, Optional[str], Dict]]:
+        """
+        Fetch definitions for multiple CURIEs from OLS.
+
+        :param curies: The CURIEs to fetch definitions for
+        :param include_metadata: Whether to include metadata (currently not supported)
+        :param include_missing: Whether to include CURIEs with no definition
+        :param lang: Optional language tag (not currently supported by this implementation)
+        :return: Iterator of (CURIE, definition, metadata) tuples
+        """
         for curie in curies:
-            yield curie, self.label_cache[curie]
+            definition = self.definition(curie, lang)
+            if definition is None and not include_missing:
+                continue
+            # Currently OLS doesn't provide metadata for definitions through the API
+            # So we're just returning an empty dict
+            yield curie, definition, {}
 
     def annotate_text(self, text: str) -> Iterator[TextAnnotation]:
         raise NotImplementedError

src/oaklib/types.py

@@ -7,4 +7,5 @@
 SUBSET_CURIE = CURIE
 CATEGORY_CURIE = CURIE
 TAXON_CURIE = CURIE
+LANGUAGE_TAG = str
 COUNT_MAP = Mapping[CURIE, int]