diff --git a/backend/src/monarch_py/api/entity.py b/backend/src/monarch_py/api/entity.py
index 83db75342..fb4002c14 100644
--- a/backend/src/monarch_py/api/entity.py
+++ b/backend/src/monarch_py/api/entity.py
@@ -81,6 +81,11 @@ def _association_table(
title="Download the results as a file",
examples=[True, False],
),
+ direct: bool = Query(
+ default=False,
+ title="Only return direct associations",
+ examples=[True, False],
+ ),
) -> Union[AssociationTableResults, str]:
"""
Retrieves association table data for a given entity and association type
@@ -99,6 +104,7 @@ def _association_table(
category=category,
q=query,
traverse_orthologs=traverse_orthologs,
+ direct=direct,
sort=sort,
offset=pagination.offset,
limit=pagination.limit,
diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py
index 4605aa942..a432af2bf 100644
--- a/backend/src/monarch_py/implementations/solr/solr_implementation.py
+++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py
@@ -463,6 +463,7 @@ def get_association_table(
entity: str,
category: AssociationCategory,
traverse_orthologs: bool = False,
+ direct: bool = False,
q: Optional[str] = None,
sort: Optional[List[str]] = None,
offset: int = 0,
@@ -480,6 +481,7 @@ def get_association_table(
query = build_association_table_query(
entity=entities,
category=category.value,
+ direct=direct,
q=q,
sort=sort,
offset=offset,
diff --git a/backend/src/monarch_py/implementations/solr/solr_query_utils.py b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
index 690a84ab6..4eb684eec 100644
--- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py
+++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py
@@ -75,7 +75,13 @@ def build_association_query(
def build_association_table_query(
- entity: List[str], category: str, q: Optional[str] = None, offset: int = 0, limit: int = 5, sort: List[str] = None
+ entity: List[str],
+ category: str,
+ direct: bool = False,
+ q: Optional[str] = None,
+ offset: int = 0,
+ limit: int = 5,
+ sort: List[str] = None,
) -> SolrQuery:
if sort is None:
sort = [
@@ -88,7 +94,7 @@ def build_association_table_query(
]
query = build_association_query(
- entity=entity, category=[category], q=q, sort=sort, offset=offset, limit=limit, direct=False
+ entity=entity, category=[category], q=q, sort=sort, offset=offset, limit=limit, direct=direct
)
return query
diff --git a/backend/tests/api/test_entity_router.py b/backend/tests/api/test_entity_router.py
index 2ecc4f6c3..0b9cd6b11 100644
--- a/backend/tests/api/test_entity_router.py
+++ b/backend/tests/api/test_entity_router.py
@@ -25,6 +25,7 @@ def test_association_table(mock_get_assoc_table):
category=AssociationCategory.DISEASE_TO_PHENOTYPIC_FEATURE_ASSOCIATION,
q=None,
traverse_orthologs=False,
+ direct=False,
sort=None,
offset=0,
limit=20,
diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py
index 39bd00b5e..fbc288d79 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": 1,
+ "QTime": 2,
"params": {
"facet.query": [
'(category:"biolink:DiseaseToPhenotypicFeatureAssociation") AND (subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121")',
diff --git a/backend/tests/fixtures/association_table_response.py b/backend/tests/fixtures/association_table_response.py
index 9894aa6bf..c98ca9ec8 100644
--- a/backend/tests/fixtures/association_table_response.py
+++ b/backend/tests/fixtures/association_table_response.py
@@ -5,7 +5,7 @@
def association_table_response():
return {
"responseHeader": {
- "QTime": 0,
+ "QTime": 1,
"params": {
"mm": "100%",
"q": "*:*",
diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
index 4c068982d..2784ba9d8 100644
--- a/backend/tests/fixtures/autocomplete_response.py
+++ b/backend/tests/fixtures/autocomplete_response.py
@@ -5,7 +5,7 @@
def autocomplete_response():
return {
"responseHeader": {
- "QTime": 0,
+ "QTime": 1,
"params": {
"mm": "100%",
"q": "fanc",
diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py
index 0d5941576..4ec64a0a2 100644
--- a/backend/tests/fixtures/search_response.py
+++ b/backend/tests/fixtures/search_response.py
@@ -5,7 +5,7 @@
def search_response():
return {
"responseHeader": {
- "QTime": 0,
+ "QTime": 4,
"params": {
"mm": "100%",
"q": "fanconi",
diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json
index a000d4738..1b8f5d773 100644
--- a/frontend/fixtures/phenotype-explorer-compare.json
+++ b/frontend/fixtures/phenotype-explorer-compare.json
@@ -1,12 +1,12 @@
{
"subject_termset": {
- "MP:0010771": {
- "id": "MP:0010771",
- "label": "integument phenotype"
- },
"MP:0002169": {
"id": "MP:0002169",
"label": "no abnormal phenotype detected"
+ },
+ "MP:0010771": {
+ "id": "MP:0010771",
+ "label": "integument phenotype"
}
},
"object_termset": {
@@ -77,8 +77,8 @@
"HP:0004325": {
"match_source": "HP:0004325",
"match_source_label": "Decreased body weight",
- "match_target": "MP:0010771",
- "match_target_label": "integument phenotype",
+ "match_target": "MP:0002169",
+ "match_target_label": "no abnormal phenotype detected",
"score": 1.5518735174643892,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -86,7 +86,7 @@
"subject_id": "HP:0004325",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0010771",
+ "object_id": "MP:0002169",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0001003",
@@ -95,10 +95,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 1.5518735174643892,
- "jaccard_similarity": 0.24,
+ "jaccard_similarity": 0.23076923076923078,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 0.6102865263066631
+ "phenodigm_score": 0.5984351743308522
},
"score_metric": "ancestor_information_content"
}
diff --git a/frontend/fixtures/phenotype-explorer-multi-compare.json b/frontend/fixtures/phenotype-explorer-multi-compare.json
index 1c4cfc932..389fa8c1a 100644
--- a/frontend/fixtures/phenotype-explorer-multi-compare.json
+++ b/frontend/fixtures/phenotype-explorer-multi-compare.json
@@ -22,57 +22,57 @@
"has_phenotype_closure_label": [],
"has_phenotype_count": null
},
- "score": 8.60883472685004,
+ "score": 8.608834726850038,
"similarity": {
"subject_termset": {
"HP:0001533": { "id": "HP:0001533", "label": "Slender build" },
- "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" },
- "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" },
- "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" },
"HP:0002020": {
"id": "HP:0002020",
"label": "Gastroesophageal reflux"
},
- "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" },
+ "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" },
"HP:0004944": {
"id": "HP:0004944",
"label": "Dilatation of the cerebral artery"
- }
+ },
+ "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" },
+ "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" },
+ "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" }
},
"object_termset": {
"MP:0011960": {
"id": "MP:0011960",
"label": "abnormal eye anterior chamber depth"
},
- "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" },
"MP:0008489": {
"id": "MP:0008489",
"label": "slow postnatal weight gain"
},
- "MP:0003291": {
- "id": "MP:0003291",
- "label": "interstinal hyperperistalsis"
- },
+ "MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" },
+ "MP:0001262": { "id": "MP:0001262", "label": "decreased body weight" },
"MP:0011962": {
"id": "MP:0011962",
"label": "increased cornea thickness"
},
- "MP:0011965": {
- "id": "MP:0011965",
- "label": "decreased total retina thickness"
- },
"MP:0003731": {
"id": "MP:0003731",
"label": "abnormal retina outer nuclear layer morphology"
},
- "MP:0001262": { "id": "MP:0001262", "label": "decreased body weight" }
+ "MP:0003291": {
+ "id": "MP:0003291",
+ "label": "interstinal hyperperistalsis"
+ },
+ "MP:0011965": {
+ "id": "MP:0011965",
+ "label": "decreased total retina thickness"
+ }
},
"subject_best_matches": {
"HP:0001533": {
"match_source": "HP:0001533",
"match_source_label": "Slender build",
- "match_target": "MP:0001262",
- "match_target_label": "decreased body weight",
+ "match_target": "MP:0008489",
+ "match_target_label": "slow postnatal weight gain",
"score": 13.667892510789482,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -80,7 +80,7 @@
"subject_id": "HP:0001533",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0001262",
+ "object_id": "MP:0008489",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0082794",
@@ -89,18 +89,18 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 13.667892510789482,
- "jaccard_similarity": 0.40384615384615385,
+ "jaccard_similarity": 0.38333333333333336,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 2.34940967514501
+ "phenodigm_score": 2.2889645684900053
},
"score_metric": "ancestor_information_content"
},
"HP:0001763": {
"match_source": "HP:0001763",
"match_source_label": "Pes planus",
- "match_target": "MP:0011962",
- "match_target_label": "increased cornea thickness",
+ "match_target": "MP:0002834",
+ "match_target_label": "decreased heart weight",
"score": 3.066606173373863,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -108,7 +108,7 @@
"subject_id": "HP:0001763",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0011962",
+ "object_id": "MP:0002834",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0015280",
@@ -117,10 +117,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 3.066606173373863,
- "jaccard_similarity": 0.16049382716049382,
+ "jaccard_similarity": 0.203125,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 0.7015492578278222
+ "phenodigm_score": 0.7892429150563
},
"score_metric": "ancestor_information_content"
},
@@ -211,8 +211,8 @@
"HP:0010749": {
"match_source": "HP:0010749",
"match_source_label": "Blepharochalasis",
- "match_target": "MP:0011965",
- "match_target_label": "decreased total retina thickness",
+ "match_target": "MP:0003731",
+ "match_target_label": "abnormal retina outer nuclear layer morphology",
"score": 6.6792078240173165,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -220,7 +220,7 @@
"subject_id": "HP:0010749",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0011965",
+ "object_id": "MP:0003731",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0087924",
@@ -229,10 +229,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 6.6792078240173165,
- "jaccard_similarity": 0.24324324324324326,
+ "jaccard_similarity": 0.23076923076923078,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.2746262877446148
+ "phenodigm_score": 1.2415134520802842
},
"score_metric": "ancestor_information_content"
},
@@ -281,8 +281,8 @@
"object_id": "HP:0001533",
"object_label": null,
"object_source": null,
- "ancestor_id": "UPHENO:0082794",
- "ancestor_label": "Decreased multicellular organism mass",
+ "ancestor_id": "UPHENO:0054299",
+ "ancestor_label": "decreased multicellular organism mass",
"ancestor_source": null,
"object_information_content": null,
"subject_information_content": null,
@@ -325,8 +325,8 @@
"MP:0003291": {
"match_source": "MP:0003291",
"match_source_label": "interstinal hyperperistalsis",
- "match_target": "HP:0012450",
- "match_target_label": "Chronic constipation",
+ "match_target": "HP:0002020",
+ "match_target_label": "Gastroesophageal reflux",
"score": 9.97713534604573,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -334,7 +334,7 @@
"subject_id": "MP:0003291",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0012450",
+ "object_id": "HP:0002020",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0002443",
@@ -343,10 +343,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 9.97713534604573,
- "jaccard_similarity": 0.4117647058823529,
+ "jaccard_similarity": 0.3684210526315789,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 2.026877450985369
+ "phenodigm_score": 1.9172341292700534
},
"score_metric": "ancestor_information_content"
},
@@ -393,8 +393,8 @@
"object_id": "HP:0001533",
"object_label": null,
"object_source": null,
- "ancestor_id": "UPHENO:0054299",
- "ancestor_label": "decreased multicellular organism mass",
+ "ancestor_id": "UPHENO:0082794",
+ "ancestor_label": "Decreased multicellular organism mass",
"ancestor_source": null,
"object_information_content": null,
"subject_information_content": null,
@@ -491,7 +491,7 @@
"score_metric": "ancestor_information_content"
}
},
- "average_score": 8.60883472685004,
+ "average_score": 8.608834726850038,
"best_score": 13.667892510789482,
"metric": "AncestorInformationContent"
}
@@ -522,16 +522,19 @@
"score": 7.343905449061466,
"similarity": {
"subject_termset": {
- "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" },
- "HP:0004944": {
- "id": "HP:0004944",
- "label": "Dilatation of the cerebral artery"
+ "HP:0002020": {
+ "id": "HP:0002020",
+ "label": "Gastroesophageal reflux"
},
"HP:0001533": { "id": "HP:0001533", "label": "Slender build" },
- "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" },
"HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis" },
"HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm" },
- "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux" }
+ "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation" },
+ "HP:0004944": {
+ "id": "HP:0004944",
+ "label": "Dilatation of the cerebral artery"
+ },
+ "HP:0001763": { "id": "HP:0001763", "label": "Pes planus" }
},
"object_termset": {
"MP:0004022": {
@@ -539,37 +542,37 @@
"label": "abnormal cone electrophysiology"
},
"MP:0002834": { "id": "MP:0002834", "label": "decreased heart weight" },
- "MP:0003026": {
- "id": "MP:0003026",
- "label": "decreased vasoconstriction"
- },
- "MP:0004021": {
- "id": "MP:0004021",
- "label": "abnormal rod electrophysiology"
- },
"MP:0006264": {
"id": "MP:0006264",
"label": "decreased systemic arterial systolic blood pressure"
},
- "MP:0000230": {
- "id": "MP:0000230",
- "label": "abnormal systemic arterial blood pressure"
- },
"MP:0000233": {
"id": "MP:0000233",
"label": "abnormal blood flow velocity"
},
+ "MP:0000272": {
+ "id": "MP:0000272",
+ "label": "abnormal aorta morphology"
+ },
+ "MP:0000230": {
+ "id": "MP:0000230",
+ "label": "abnormal systemic arterial blood pressure"
+ },
"MP:0009862": {
"id": "MP:0009862",
"label": "abnormal aorta elastic tissue morphology"
},
+ "MP:0004021": {
+ "id": "MP:0004021",
+ "label": "abnormal rod electrophysiology"
+ },
"MP:0003070": {
"id": "MP:0003070",
"label": "increased vascular permeability"
},
- "MP:0000272": {
- "id": "MP:0000272",
- "label": "abnormal aorta morphology"
+ "MP:0003026": {
+ "id": "MP:0003026",
+ "label": "decreased vasoconstriction"
}
},
"subject_best_matches": {
@@ -688,8 +691,8 @@
"HP:0004944": {
"match_source": "HP:0004944",
"match_source_label": "Dilatation of the cerebral artery",
- "match_target": "MP:0009862",
- "match_target_label": "abnormal aorta elastic tissue morphology",
+ "match_target": "MP:0000272",
+ "match_target_label": "abnormal aorta morphology",
"score": 9.101342047182207,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -697,7 +700,7 @@
"subject_id": "HP:0004944",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0009862",
+ "object_id": "MP:0000272",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0087334",
@@ -706,18 +709,18 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 9.101342047182207,
- "jaccard_similarity": 0.25757575757575757,
+ "jaccard_similarity": 0.2807017543859649,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.5311058332979641
+ "phenodigm_score": 1.5983624995321914
},
"score_metric": "ancestor_information_content"
},
"HP:0010749": {
"match_source": "HP:0010749",
"match_source_label": "Blepharochalasis",
- "match_target": "MP:0004022",
- "match_target_label": "abnormal cone electrophysiology",
+ "match_target": "MP:0004021",
+ "match_target_label": "abnormal rod electrophysiology",
"score": 5.771757578540516,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -725,7 +728,7 @@
"subject_id": "HP:0010749",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0004022",
+ "object_id": "MP:0004021",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0075997",
@@ -744,8 +747,8 @@
"HP:0012450": {
"match_source": "HP:0012450",
"match_source_label": "Chronic constipation",
- "match_target": "MP:0003070",
- "match_target_label": "increased vascular permeability",
+ "match_target": "MP:0003026",
+ "match_target_label": "decreased vasoconstriction",
"score": 5.132448071645384,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -753,7 +756,7 @@
"subject_id": "HP:0012450",
"subject_label": null,
"subject_source": null,
- "object_id": "MP:0003070",
+ "object_id": "MP:0003026",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0002332",
@@ -762,10 +765,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 5.132448071645384,
- "jaccard_similarity": 0.2926829268292683,
+ "jaccard_similarity": 0.2727272727272727,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.2256344982940082
+ "phenodigm_score": 1.1831139273097055
},
"score_metric": "ancestor_information_content"
}
@@ -774,8 +777,8 @@
"MP:0000230": {
"match_source": "MP:0000230",
"match_source_label": "abnormal systemic arterial blood pressure",
- "match_target": "HP:0002616",
- "match_target_label": "Aortic root aneurysm",
+ "match_target": "HP:0004944",
+ "match_target_label": "Dilatation of the cerebral artery",
"score": 7.3467487024345575,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -783,7 +786,7 @@
"subject_id": "MP:0000230",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0002616",
+ "object_id": "HP:0004944",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0080362",
@@ -792,18 +795,18 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 7.3467487024345575,
- "jaccard_similarity": 0.2558139534883721,
+ "jaccard_similarity": 0.19642857142857142,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.3709124081630277
+ "phenodigm_score": 1.2012956972635551
},
"score_metric": "ancestor_information_content"
},
"MP:0000233": {
"match_source": "MP:0000233",
"match_source_label": "abnormal blood flow velocity",
- "match_target": "HP:0002616",
- "match_target_label": "Aortic root aneurysm",
+ "match_target": "HP:0004944",
+ "match_target_label": "Dilatation of the cerebral artery",
"score": 7.3467487024345575,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -811,7 +814,7 @@
"subject_id": "MP:0000233",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0002616",
+ "object_id": "HP:0004944",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0080362",
@@ -820,10 +823,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 7.3467487024345575,
- "jaccard_similarity": 0.23404255319148937,
+ "jaccard_similarity": 0.18333333333333332,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.311278698055469
+ "phenodigm_score": 1.160561902174834
},
"score_metric": "ancestor_information_content"
},
@@ -886,8 +889,8 @@
"MP:0003026": {
"match_source": "MP:0003026",
"match_source_label": "decreased vasoconstriction",
- "match_target": "HP:0004944",
- "match_target_label": "Dilatation of the cerebral artery",
+ "match_target": "HP:0002616",
+ "match_target_label": "Aortic root aneurysm",
"score": 7.3467487024345575,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -895,7 +898,7 @@
"subject_id": "MP:0003026",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0004944",
+ "object_id": "HP:0002616",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0080362",
@@ -904,10 +907,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 7.3467487024345575,
- "jaccard_similarity": 0.17391304347826086,
+ "jaccard_similarity": 0.21428571428571427,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.1303519038380736
+ "phenodigm_score": 1.2547124345358316
},
"score_metric": "ancestor_information_content"
},
@@ -998,8 +1001,8 @@
"MP:0006264": {
"match_source": "MP:0006264",
"match_source_label": "decreased systemic arterial systolic blood pressure",
- "match_target": "HP:0002616",
- "match_target_label": "Aortic root aneurysm",
+ "match_target": "HP:0004944",
+ "match_target_label": "Dilatation of the cerebral artery",
"score": 7.3467487024345575,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -1007,7 +1010,7 @@
"subject_id": "MP:0006264",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0002616",
+ "object_id": "HP:0004944",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0080362",
@@ -1016,10 +1019,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 7.3467487024345575,
- "jaccard_similarity": 0.24444444444444444,
+ "jaccard_similarity": 0.1896551724137931,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 1.340101453263729
+ "phenodigm_score": 1.1804020043362502
},
"score_metric": "ancestor_information_content"
},
diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json
index b203ef702..99ff9d3ce 100644
--- a/frontend/fixtures/phenotype-explorer-search.json
+++ b/frontend/fixtures/phenotype-explorer-search.json
@@ -97,8 +97,8 @@
}
},
"object_termset": {
- "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" },
- "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }
+ "HP:0002104": { "id": "HP:0002104", "label": "Apnea" },
+ "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }
},
"subject_best_matches": {
"ZP:0018569": {
@@ -302,18 +302,18 @@
"score": 7.011754466426716,
"similarity": {
"subject_termset": {
- "ZP:0018568": {
- "id": "ZP:0018568",
- "label": "primitive hemopoiesis absent, abnormal"
- },
"ZP:0018569": {
"id": "ZP:0018569",
"label": "myeloid cell development absent, abnormal"
+ },
+ "ZP:0018568": {
+ "id": "ZP:0018568",
+ "label": "primitive hemopoiesis absent, abnormal"
}
},
"object_termset": {
- "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" },
- "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }
+ "HP:0002104": { "id": "HP:0002104", "label": "Apnea" },
+ "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }
},
"subject_best_matches": {
"ZP:0018568": {
@@ -377,8 +377,8 @@
"HP:0002104": {
"match_source": "HP:0002104",
"match_source_label": "Apnea",
- "match_target": "ZP:0018569",
- "match_target_label": "myeloid cell development absent, abnormal",
+ "match_target": "ZP:0018568",
+ "match_target_label": "primitive hemopoiesis absent, abnormal",
"score": 8.79057503056431,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -386,7 +386,7 @@
"subject_id": "HP:0002104",
"subject_label": null,
"subject_source": null,
- "object_id": "ZP:0018569",
+ "object_id": "ZP:0018568",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0034024",
@@ -618,8 +618,8 @@
"HP:0002104": {
"match_source": "HP:0002104",
"match_source_label": "Apnea",
- "match_target": "ZP:0018568",
- "match_target_label": "primitive hemopoiesis absent, abnormal",
+ "match_target": "ZP:0018569",
+ "match_target_label": "myeloid cell development absent, abnormal",
"score": 8.79057503056431,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -627,7 +627,7 @@
"subject_id": "HP:0002104",
"subject_label": null,
"subject_source": null,
- "object_id": "ZP:0018568",
+ "object_id": "ZP:0018569",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0034024",
@@ -801,8 +801,8 @@
}
},
"object_termset": {
- "HP:0002104": { "id": "HP:0002104", "label": "Apnea" },
- "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }
+ "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" },
+ "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }
},
"subject_best_matches": {
"ZP:0018568": {
@@ -866,8 +866,8 @@
"HP:0002104": {
"match_source": "HP:0002104",
"match_source_label": "Apnea",
- "match_target": "ZP:0018568",
- "match_target_label": "primitive hemopoiesis absent, abnormal",
+ "match_target": "ZP:0018569",
+ "match_target_label": "myeloid cell development absent, abnormal",
"score": 8.79057503056431,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -875,7 +875,7 @@
"subject_id": "HP:0002104",
"subject_label": null,
"subject_source": null,
- "object_id": "ZP:0018568",
+ "object_id": "ZP:0018569",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0034024",
@@ -894,8 +894,8 @@
"HP:0012378": {
"match_source": "HP:0012378",
"match_source_label": "Fatigue",
- "match_target": "ZP:0018568",
- "match_target_label": "primitive hemopoiesis absent, abnormal",
+ "match_target": "ZP:0018569",
+ "match_target_label": "myeloid cell development absent, abnormal",
"score": 1.6752927740139332,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -903,7 +903,7 @@
"subject_id": "HP:0012378",
"subject_label": null,
"subject_source": null,
- "object_id": "ZP:0018568",
+ "object_id": "ZP:0018569",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0001005",
@@ -1039,18 +1039,18 @@
"score": 7.011754466426716,
"similarity": {
"subject_termset": {
- "ZP:0018569": {
- "id": "ZP:0018569",
- "label": "myeloid cell development absent, abnormal"
- },
"ZP:0018568": {
"id": "ZP:0018568",
"label": "primitive hemopoiesis absent, abnormal"
+ },
+ "ZP:0018569": {
+ "id": "ZP:0018569",
+ "label": "myeloid cell development absent, abnormal"
}
},
"object_termset": {
- "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" },
- "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }
+ "HP:0002104": { "id": "HP:0002104", "label": "Apnea" },
+ "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }
},
"subject_best_matches": {
"ZP:0018568": {
@@ -1452,8 +1452,8 @@
"HP:0012378": {
"match_source": "HP:0012378",
"match_source_label": "Fatigue",
- "match_target": "ZP:0000945",
- "match_target_label": "pigment cell quality, abnormal",
+ "match_target": "ZP:0100294",
+ "match_target_label": "visual perception absent, abnormal",
"score": 1.6752927740139332,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -1461,7 +1461,7 @@
"subject_id": "HP:0012378",
"subject_label": null,
"subject_source": null,
- "object_id": "ZP:0000945",
+ "object_id": "ZP:0100294",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0001005",
@@ -1470,10 +1470,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 1.6752927740139332,
- "jaccard_similarity": 0.42105263157894735,
+ "jaccard_similarity": 0.4444444444444444,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 0.8398728660718605
+ "phenodigm_score": 0.8628873427211774
},
"score_metric": "ancestor_information_content"
}
@@ -1568,13 +1568,13 @@
"score": 5.232933902289122,
"similarity": {
"subject_termset": {
- "ZP:0001841": {
- "id": "ZP:0001841",
- "label": "visual behavior quality, abnormal"
- },
"ZP:0015039": {
"id": "ZP:0015039",
"label": "visual behavior absent, abnormal"
+ },
+ "ZP:0001841": {
+ "id": "ZP:0001841",
+ "label": "visual behavior quality, abnormal"
}
},
"object_termset": {
@@ -1585,8 +1585,8 @@
"ZP:0001841": {
"match_source": "ZP:0001841",
"match_source_label": "visual behavior quality, abnormal",
- "match_target": "HP:0012378",
- "match_target_label": "Fatigue",
+ "match_target": "HP:0002104",
+ "match_target_label": "Apnea",
"score": 1.6752927740139332,
"match_subsumer": null,
"match_subsumer_label": null,
@@ -1594,7 +1594,7 @@
"subject_id": "ZP:0001841",
"subject_label": null,
"subject_source": null,
- "object_id": "HP:0012378",
+ "object_id": "HP:0002104",
"object_label": null,
"object_source": null,
"ancestor_id": "UPHENO:0001005",
@@ -1603,10 +1603,10 @@
"object_information_content": null,
"subject_information_content": null,
"ancestor_information_content": 1.6752927740139332,
- "jaccard_similarity": 0.47058823529411764,
+ "jaccard_similarity": 0.2962962962962963,
"cosine_similarity": null,
"dice_similarity": null,
- "phenodigm_score": 0.8879037504843663
+ "phenodigm_score": 0.7045445650576523
},
"score_metric": "ancestor_information_content"
},
@@ -1931,8 +1931,8 @@
}
},
"object_termset": {
- "HP:0002104": { "id": "HP:0002104", "label": "Apnea" },
- "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }
+ "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" },
+ "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }
},
"subject_best_matches": {
"ZP:0005756": {
@@ -2435,8 +2435,8 @@
}
},
"object_termset": {
- "HP:0002104": { "id": "HP:0002104", "label": "Apnea" },
- "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" }
+ "HP:0012378": { "id": "HP:0012378", "label": "Fatigue" },
+ "HP:0002104": { "id": "HP:0002104", "label": "Apnea" }
},
"subject_best_matches": {
"ZP:0001432": {
diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index 580a96850..13f199c11 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -9,6 +9,7 @@ export const getAssociations = async (
offset = 0,
limit = 10,
traverseOrthologs = false,
+ direct = "false",
search?: string,
sort: Sort = null,
) => {
@@ -18,6 +19,7 @@ export const getAssociations = async (
limit,
query: search || "",
traverse_orthologs: !!traverseOrthologs,
+ direct: direct,
sort: sort
? `${sort.key} ${sort.direction === "up" ? "asc" : "desc"}`
: null,
@@ -38,6 +40,7 @@ export const downloadAssociations = async (
nodeId = "",
associationCategory = "",
traverseOrthologs = false,
+ direct = "false",
search?: string,
sort: Sort = null,
) => {
@@ -46,6 +49,7 @@ export const downloadAssociations = async (
limit: maxDownload,
query: search || "",
traverse_orthologs: !!traverseOrthologs,
+ direct: direct,
sort: sort
? `${sort.key} ${sort.direction === "up" ? "asc" : "desc"}`
: null,
diff --git a/frontend/src/pages/node/AssociationsTable.vue b/frontend/src/pages/node/AssociationsTable.vue
index 5c5c52595..602101610 100644
--- a/frontend/src/pages/node/AssociationsTable.vue
+++ b/frontend/src/pages/node/AssociationsTable.vue
@@ -131,6 +131,7 @@ type Props = {
category: Option;
/** include orthologs */
includeOrthologs: boolean;
+ direct: Option;
/** selected association */
association?: DirectionalAssociation;
};
@@ -288,12 +289,16 @@ const {
if (!props.node.association_counts.length)
throw Error("No association info available");
/** get association data */
+ if (fresh) {
+ start.value = 0;
+ }
const response = await getAssociations(
props.node.id,
props.category.id,
start.value,
perPage.value,
props.includeOrthologs,
+ props.direct.id,
search.value,
sort.value,
);
@@ -322,6 +327,7 @@ async function download() {
props.node.id,
props.category.id,
props.includeOrthologs,
+ props.direct.id,
search.value,
sort.value,
);
@@ -375,6 +381,10 @@ watch(
() => props.includeOrthologs,
async () => await queryAssociations(true),
);
+watch(
+ () => props.direct,
+ async () => await queryAssociations(true),
+);
watch(
[perPage, start, search, sort],
async () => await queryAssociations(false),
diff --git a/frontend/src/pages/node/SectionAssociations.vue b/frontend/src/pages/node/SectionAssociations.vue
index 07a32ea61..9c1633ca0 100644
--- a/frontend/src/pages/node/SectionAssociations.vue
+++ b/frontend/src/pages/node/SectionAssociations.vue
@@ -15,14 +15,21 @@
- associations involving
-
-
+ :options="categoryOptions" /> associations
+ involving
+
+
+
@@ -98,6 +106,7 @@ const category = ref