diff --git a/backend/src/monarch_py/api/additional_models.py b/backend/src/monarch_py/api/additional_models.py
index a9f7b35d4..36af77884 100644
--- a/backend/src/monarch_py/api/additional_models.py
+++ b/backend/src/monarch_py/api/additional_models.py
@@ -30,5 +30,5 @@ class SemsimCompareRequest(BaseModel):
class SemsimSearchRequest(BaseModel):
termset: List[str] = Field(..., title="Termset to search")
- prefix: str = Field(..., title="Prefix to search for")
- limit: Optional[int] = Field(..., title="Limit the number of results")
+ category: SemsimSearchCategory = Field(..., title="Category to search for")
+ limit: Optional[int] = Field(10, title="Limit the number of results", ge=1, le=50)
diff --git a/backend/src/monarch_py/api/semsim.py b/backend/src/monarch_py/api/semsim.py
index 26fe797bb..4a168989a 100644
--- a/backend/src/monarch_py/api/semsim.py
+++ b/backend/src/monarch_py/api/semsim.py
@@ -1,4 +1,4 @@
-from fastapi import APIRouter, HTTPException, Path, Query
+from fastapi import APIRouter, Path, Query
from monarch_py.api.additional_models import SemsimCompareRequest, SemsimSearchRequest, SemsimSearchCategory
from monarch_py.api.config import semsimian
@@ -54,14 +54,14 @@ def _post_compare(request: SemsimCompareRequest):
@router.get("/search/{termset}/{prefix}")
def _search(
termset: str = Path(..., title="Termset to search"),
- prefix: str = Path(..., title="Prefix to search for"),
- limit: int = Query(default=10, ge=0, le=500),
+ category: SemsimSearchCategory = Path(..., title="Category of entities to search for"),
+ limit: int = Query(default=10, ge=1, le=50),
):
"""Search for terms in a termset
Args:
- termset (str, optional): Termset to search. Defaults to "".
- prefix (str, optional): Prefix to search for. Defaults to "".
+ termset (str, optional): Comma separated list of term IDs to find matches for.
+ category (str, optional): Category of entities to search for.
limit (int, optional): Limit the number of results. Defaults to 10.
Returns:
@@ -72,11 +72,11 @@ def _search(
f"""
Running semsim search:
termset: {termset}
- prefix: {prefix}
+ category: {category}
"""
)
-
- results = semsimian().search(termset=termset.split(","), prefix=parse_similarity_prefix(prefix), limit=limit)
+
+ results = semsimian().search(termset=termset.split(","), prefix=parse_similarity_prefix(category), limit=limit)
return results
@@ -88,10 +88,10 @@ def _post_search(request: SemsimSearchRequest):
Example:
{
- "termset": ["HP:0000001", "HP:0000002"],
- "prefix": "ZFIN",
+ "termset": ["HP:0002104", "HP:0012378", "HP:0012378", "HP:0012378"],
+ "category": "Human Diseases",
"limit": 5
}
"""
- return semsimian().search(request.termset, parse_similarity_prefix(request.prefix), request.limit)
+ return semsimian().search(request.termset, parse_similarity_prefix(request.category.value), request.limit)
diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
index a19f9b0e4..b5dd2bad8 100644
--- a/backend/tests/fixtures/association_counts_response.py
+++ b/backend/tests/fixtures/association_counts_response.py
@@ -5,7 +5,7 @@
def association_counts_response():
return {
"responseHeader": {
- "QTime": 2,
+ "QTime": 1,
"params": {
"facet.query": [
'(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
diff --git a/backend/tests/fixtures/phenotype_explorer_search.py b/backend/tests/fixtures/phenotype_explorer_search.py
index 49a5081a1..3434ca470 100644
--- a/backend/tests/fixtures/phenotype_explorer_search.py
+++ b/backend/tests/fixtures/phenotype_explorer_search.py
@@ -4,790 +4,1070 @@
@pytest.fixture
def phenotype_explorer_search():
return [
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0002909": {"id": "ZP:0002909", "label": "whole organism dwarf-like, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0002909": {
- "match_source": "ZP:0002909",
- "match_source_label": "whole organism dwarf-like, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0002909": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4444444444444444",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.198054183387448",
- "subject_id": "ZP:0002909",
- }
- },
- "object_termset": [
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0002909",
- "match_target_label": "whole organism dwarf-like, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0002909",
- "match_target_label": "whole organism dwarf-like, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0002909",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
- },
- "HP:0000002": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4444444444444444",
- "object_id": "ZP:0002909",
- "phenodigm_score": "2.198054183387448",
- "subject_id": "HP:0000002",
- },
- },
- "average_score": 8.153058700868163,
- "best_score": 10.870744934490885,
- "metric": "ancestor_information_content",
- },
- "ZFIN:ZDB-GENE-070117-1426",
- ],
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0000473": {"id": "ZP:0000473", "label": "whole organism decreased length, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0000473": {
- "match_source": "ZP:0000473",
- "match_source_label": "whole organism decreased length, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0000473": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "ZP:0000473",
- }
- },
- "object_termset": [
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0000473",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
- },
- "HP:0000002": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "ZP:0000473",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "HP:0000002",
- },
- },
- "average_score": 8.153058700868163,
- "best_score": 10.870744934490885,
- "metric": "ancestor_information_content",
- },
- "ZFIN:ZDB-GENE-081022-128",
- ],
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0000473": {"id": "ZP:0000473", "label": "whole organism decreased length, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0000473": {
- "match_source": "ZP:0000473",
- "match_source_label": "whole organism decreased length, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0000473": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "ZP:0000473",
- }
- },
- "object_termset": [
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0000473",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
- },
- "HP:0000002": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "ZP:0000473",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "HP:0000002",
- },
- },
- "average_score": 8.153058700868163,
- "best_score": 10.870744934490885,
- "metric": "ancestor_information_content",
- },
- "ZFIN:ZDB-GENE-111209-1",
- ],
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0000473": {"id": "ZP:0000473", "label": "whole organism decreased length, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0000473": {
- "match_source": "ZP:0000473",
- "match_source_label": "whole organism decreased length, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0000473": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "ZP:0000473",
- }
- },
- "object_termset": [
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0000473",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
- },
- "HP:0000002": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "ZP:0000473",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "HP:0000002",
- },
- },
- "average_score": 8.153058700868163,
- "best_score": 10.870744934490885,
- "metric": "ancestor_information_content",
- },
- "ZFIN:ZDB-GENE-070117-1424",
- ],
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0000473": {"id": "ZP:0000473", "label": "whole organism decreased length, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0000473": {
- "match_source": "ZP:0000473",
- "match_source_label": "whole organism decreased length, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0000473": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "ZP:0000473",
- }
- },
- "object_termset": [
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0000473",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
- },
- "HP:0000002": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "ZP:0000473",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "HP:0000002",
- },
- },
- "average_score": 8.153058700868163,
- "best_score": 10.870744934490885,
- "metric": "ancestor_information_content",
- },
- "ZFIN:ZDB-GENE-030131-4487",
- ],
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0000473": {"id": "ZP:0000473", "label": "whole organism decreased length, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0000473": {
- "match_source": "ZP:0000473",
- "match_source_label": "whole organism decreased length, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0000473": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "ZP:0000473",
- }
- },
- "object_termset": [
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0000473",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
- },
- "HP:0000002": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "ZP:0000473",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "HP:0000002",
- },
- },
- "average_score": 8.153058700868163,
- "best_score": 10.870744934490885,
- "metric": "ancestor_information_content",
- },
- "ZFIN:ZDB-GENE-070117-1594",
- ],
- [
- 8.153058700868163,
- {
- "subject_termset": [
- {"ZP:0000473": {"id": "ZP:0000473", "label": "whole organism decreased length, abnormal (ZPO)"}}
- ],
- "subject_best_matches": {
- "ZP:0000473": {
- "match_source": "ZP:0000473",
- "match_source_label": "whole organism decreased length, abnormal (ZPO)",
- "match_target": "HP:0000002",
- "match_target_label": "Abnormality of body height (HPO)",
- "score": "10.870744934490885",
- }
- },
- "subject_best_matches_similarity_map": {
- "ZP:0000473": {
- "ancestor_id": "UPHENO:0075159",
- "ancestor_information_content": "10.870744934490885",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0.4",
- "object_id": "HP:0000002",
- "phenodigm_score": "2.0852572919897328",
- "subject_id": "ZP:0000473",
- }
- },
- "object_termset": [
- {"HP:0000001": {"id": "HP:0000001", "label": "All (HPO)"}},
- {"HP:0000002": {"id": "HP:0000002", "label": "Abnormality of body height (HPO)"}},
- ],
- "object_best_matches": {
- "HP:0000001": {
- "match_source": "HP:0000001",
- "match_source_label": "All (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "0",
- },
- "HP:0000002": {
- "match_source": "HP:0000002",
- "match_source_label": "Abnormality of body height (HPO)",
- "match_target": "ZP:0000473",
- "match_target_label": "whole organism decreased length, abnormal (ZPO)",
- "score": "10.870744934490885",
- },
- },
- "object_best_matches_similarity_map": {
- "HP:0000001": {
- "ancestor_id": "NO_ANCESTOR_FOUND",
- "ancestor_information_content": "0",
- "ancestor_label": "",
- "cosine_similarity": "NaN",
- "jaccard_similarity": "0",
- "object_id": "ZP:0000473",
- "phenodigm_score": "0",
- "subject_id": "HP:0000001",
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+ "HP:0000002": BestMatch(
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+ metric="ancestor_information_content",
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+ SemsimSearchResult(
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+ similarity=TermSetPairwiseSimilarity(
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+ },
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+ match_source_label="whole organism decreased length, abnormal (ZPO)",
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+ phenodigm_score=2.0852572919897328,
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+ object_best_matches={
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+ match_target_label="whole organism decreased length, abnormal (ZPO)",
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+ "HP:0000002": BestMatch(
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+ match_source_label="Abnormality of body height (HPO)",
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+ average_score=8.153058700868163,
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+ metric="ancestor_information_content",
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+ SemsimSearchResult(
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+ similarity=TermSetPairwiseSimilarity(
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+ "ZP:0000473": BestMatch(
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+ match_source_label="whole organism decreased length, abnormal (ZPO)",
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+ phenodigm_score=2.0852572919897328,
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+ "HP:0000002": BestMatch(
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+ match_source_label="Abnormality of body height (HPO)",
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+ match_target_label="whole organism decreased length, abnormal (ZPO)",
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+ similarity=TermPairwiseSimilarity(
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+ SemsimSearchResult(
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+ match_source_label="whole organism decreased length, abnormal (ZPO)",
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+ similarity=TermPairwiseSimilarity(
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+ "HP:0000002": BestMatch(
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+ match_source_label="Abnormality of body height (HPO)",
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+ SemsimSearchResult(
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+ object_best_matches={
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diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
index 07e1cdf67..5bf67baca 100644
--- a/backend/tests/fixtures/search_response.py
+++ b/backend/tests/fixtures/search_response.py
@@ -5,7 +5,7 @@
def search_response():
return {
"responseHeader": {
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+ "QTime": 2,
"params": {
"mm": "100%",
"q": "fanconi",
diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json
index b9b077c65..2083a07b5 100644
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+}
diff --git a/frontend/src/api/model.ts b/frontend/src/api/model.ts
index 163510f07..d45a10453 100644
--- a/frontend/src/api/model.ts
+++ b/frontend/src/api/model.ts
@@ -519,18 +519,18 @@ export interface TermPairwiseSimilarity extends PairwiseSimilarity {
ancestor_label?: string,
ancestor_source?: string,
/** The IC of the object */
- object_information_content?: string,
+ object_information_content?: number,
/** The IC of the subject */
- subject_information_content?: string,
+ subject_information_content?: number,
/** The IC of the object */
- ancestor_information_content?: string,
+ ancestor_information_content?: number,
/** The number of concepts in the intersection divided by the number in the union */
- jaccard_similarity?: string,
+ jaccard_similarity?: number,
/** the dot product of two node embeddings divided by the product of their lengths */
cosine_similarity?: number,
- dice_similarity?: string,
+ dice_similarity?: number,
/** the geometric mean of the jaccard similarity and the information content */
- phenodigm_score?: string,
+ phenodigm_score?: number,
};
/**
* A simple pairwise similarity between two sets of concepts/terms
diff --git a/frontend/src/components/AppPredicateBadge.vue b/frontend/src/components/AppPredicateBadge.vue
index 82b0756b0..52ca3caa4 100644
--- a/frontend/src/components/AppPredicateBadge.vue
+++ b/frontend/src/components/AppPredicateBadge.vue
@@ -34,8 +34,8 @@ const arrowDirection = computed(() =>
? "up"
: "left"
: props.vertical
- ? "down"
- : "right",
+ ? "down"
+ : "right",
);
diff --git a/frontend/src/components/AppTable.vue b/frontend/src/components/AppTable.vue
index adfcb0e2e..be4f067a0 100644
--- a/frontend/src/components/AppTable.vue
+++ b/frontend/src/components/AppTable.vue
@@ -384,8 +384,8 @@ const widths = computed((): string =>
col.slot === "divider"
? "20px"
: expanded.value
- ? `minmax(max-content, 99999px)`
- : `${col.width || 1}fr`,
+ ? `minmax(max-content, 99999px)`
+ : `${col.width || 1}fr`,
)
.join(" "),
);
diff --git a/scripts/generate_fixtures.py b/scripts/generate_fixtures.py
index 12d5f3879..c5f4ceb6a 100644
--- a/scripts/generate_fixtures.py
+++ b/scripts/generate_fixtures.py
@@ -192,7 +192,7 @@ def main(
# fixtures['node-publication-summary'] =
# fixtures['ontologies'] =
fixtures["phenotype-explorer-compare"] = _compare(subjects="MP:0010771,MP:0002169", objects="HP:0004325")
- fixtures["phenotype-explorer-search"] = _search(termset="HP:0000001,HP:0000002", prefix="ZFIN", limit=10)
+ fixtures["phenotype-explorer-search"] = _search(termset="HP:0000001,HP:0000002", category="Zebrafish Genes", limit=10)
fixtures["search"] = si.search(q="fanconi")
# fixtures['text-annotator'] =
# fixtures['uptime'] =