upgrade to latest OAK

pyproject.toml

@@ -11,7 +11,7 @@ python = ">=3.9,<3.9.7 || >3.9.7,<4.0"
 click = "^8.1.3"
 importlib = "^1.0.4"
 openai = "^0.27.4"
-oaklib = "^0.5.4"
+oaklib = "^0.5.6"
 gilda = "^0.10.3"
 jsonlines = "^3.1.0"
 python-multipart = "^0.0.5"

src/ontogpt/engines/enrichment.py

@@ -11,7 +11,7 @@
 from oaklib import BasicOntologyInterface, get_adapter
 from pydantic import BaseModel
 
-from ontogpt.engines.knowledge_engine import KnowledgeEngine, MODEL_GPT_4
+from ontogpt.engines.knowledge_engine import MODEL_GPT_4, KnowledgeEngine
 from ontogpt.prompts.enrichment import DEFAULT_ENRICHMENT_PROMPT
 from ontogpt.templates.class_enrichment import ClassEnrichmentResult
 from ontogpt.templates.gene_description_term import GeneDescriptionTerm

src/ontogpt/engines/knowledge_engine.py

@@ -165,6 +165,10 @@ def __post_init__(self):
             self.mappers = [get_adapter("translator:")]
         self.encoding = tiktoken.encoding_for_model(self.client.model)
 
+    def set_api_key(self, key: str):
+        self.api_key = key
+        openai.api_key = key
+
     def extract_from_text(
         self, text: str, cls: ClassDefinition = None, object: OBJECT = None
     ) -> ExtractionResult:

src/ontogpt/evaluation/enrichment/eval_enrichment.py

@@ -25,7 +25,12 @@
 
 from ontogpt.engines import create_engine
 from ontogpt.engines.enrichment import ENTITY_ID, EnrichmentEngine, EnrichmentPayload
-from ontogpt.engines.knowledge_engine import MODEL_GPT_3_5_TURBO, MODEL_NAME, MODEL_TEXT_DAVINCI_003, MODEL_GPT_4
+from ontogpt.engines.knowledge_engine import (
+    MODEL_GPT_3_5_TURBO,
+    MODEL_GPT_4,
+    MODEL_NAME,
+    MODEL_TEXT_DAVINCI_003,
+)
 from ontogpt.evaluation.evaluation_engine import EvaluationEngine
 from ontogpt.templates.class_enrichment import ClassEnrichmentResult
 from ontogpt.utils.gene_set_utils import SYMBOL, GeneSet, drop_genes_from_gene_set, gene_info

src/ontogpt/templates/core.yaml

@@ -5,6 +5,8 @@ license: https://creativecommons.org/publicdomain/zero/1.0/
 prefixes:
   linkml: https://w3id.org/linkml/
   core: http://w3id.org/ontogpt/core/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  RO: http://purl.obolibrary.org/obo/RO_
 description: Core upper level
 
 default_prefix: core
@@ -127,3 +129,16 @@ classes:
       subject_text:
       object_id:
       object_text:
+
+enums:
+
+  NullDataOptions:
+    permissible_values:
+      UNSPECIFIED_METHOD_OF_ADMINISTRATION:
+        meaning: NCIT:C149701
+      NOT_APPLICABLE:
+        meaning: NCIT:C18902
+        aliases:
+          - "not applicable"
+          - "N/A"
+      NOT_MENTIONED: