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base repository: monarch-initiative/curategpt
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head repository: EBISPOT/curategpt
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compare: main
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  • 2 commits
  • 2 files changed
  • 1 contributor

Commits on Mar 12, 2025

  1. Add aliases

    @aleixpuigb
    aleixpuigb committed Mar 12, 2025
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    1efc16a View commit details

  2. Merge branch 'main' of https://github.com/EBISPOT/curategpt

    @aleixpuigb
    aleixpuigb committed Mar 12, 2025
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    70359e0 View commit details
Showing with 4 additions and 1 deletion.
  1. +1 −1 Makefile
  2. +3 −0 src/curategpt/wrappers/ontology/ontology_wrapper.py
2 changes: 1 addition & 1 deletion Makefile
View file
Original file line number Diff line number Diff line change
@@ -16,7 +16,7 @@ index_all_ont: $(patsubst %,ont-%,$(ONTS))
index_all_issues: $(patsubst %,load-github-%,$(ONTS))

ont-%:
$(CURATE) ontology index --index-fields label,definition,relationships -p $(DB_PATH) -c ont_$* -m openai: sqlite:obo:$*
$(CURATE) ontology index --index-fields label,definition,relationships,aliases -p $(DB_PATH) -c ont_$* -m openai: sqlite:obo:$*

## -- Web App --

3 changes: 3 additions & 0 deletions src/curategpt/wrappers/ontology/ontology_wrapper.py
View file
Original file line number Diff line number Diff line change
@@ -93,6 +93,8 @@ def objects(
# as may be used in references
labels = {e: lbl for e, lbl in adapter.labels(entities, allow_none=False)}
logger.info(f"Found {len(labels)} labels")
aliases = {e: adapter.entity_aliases(e) for e in entities}
logger.info(f"Found {len(aliases)} sets of aliases")
definitions = {}
if self.fetch_definitions:
for chunked_entities in chunk(selected_ids, 100):
@@ -127,6 +129,7 @@ def objects(
obj = OntologyClass(
id=shorthand,
label=labels[id],
aliases=aliases[id],
original_id=id,
aliases=aliases_by_entity.get(id, []),
)