diff --git a/backend/src/monarch_py/datamodels/solr.py b/backend/src/monarch_py/datamodels/solr.py index d39030b4b..f9025b4e5 100644 --- a/backend/src/monarch_py/datamodels/solr.py +++ b/backend/src/monarch_py/datamodels/solr.py @@ -13,26 +13,26 @@ class core(Enum): class HistoPhenoKeys(Enum): - skeletal_system = "HP:0000924" - nervous_system = "HP:0000707" - head_neck = "HP:0000152" - integument = "HP:0001574" - eye = "HP:0000478" - cardiovascular_system = "HP:0001626" - metabolism_homeostasis = "HP:0001939" - genitourinary_system = "HP:0000119" - digestive_system = "HP:0025031" - neoplasm = "HP:0002664" - blood = "HP:0001871" - immune_system = "HP:0002715" - endocrine = "HP:0000818" - musculature = "HP:0003011" - respiratory = "HP:0002086" - ear = "HP:0000598" - connective_tissue = "HP:0003549" - prenatal_or_birth = "HP:0001197" - growth = "HP:0001507" - breast = "HP:0000769" + skeletal_system = "UPHENO:0002964" # "HP:0000924" + nervous_system = "UPHENO:0004523" # "HP:0000707" + head_neck = "UPHENO:0002764" # "HP:0000152" + integument = "UPHENO:0002635" # "HP:0001574" + eye = "UPHENO:0003020" # "HP:0000478" + cardiovascular_system = "UPHENO:0080362" # "HP:0001626" + metabolism_homeostasis = "HP:0001939" # ??? No uPheno parent + genitourinary_system = "UPHENO:0002642" # "HP:0000119" + digestive_system = "UPHENO:0002833" # "HP:0025031" + neoplasm = "HP:0002664" # ??? No uPheno parent + blood = "UPHENO:0004459" # "HP:0001871" + immune_system = "UPHENO:0002948" # "HP:0002715" + endocrine = "UPHENO:0003116" # "HP:0000818" + musculature = "UPHENO:0002816" # "HP:0003011" + respiratory = "UPHENO:0004536" # "HP:0002086" + ear = "HP:0000598" # UPHENO:0002903 + connective_tissue = "UPHENO:0002712" # "HP:0003549" + prenatal_or_birth = "UPHENO:0075949" # "HP:0001197" + growth = "UPHENO:0049874" # "HP:0001507" + breast = "UPHENO:0003013" # "HP:0000769" class SolrQuery(BaseModel): diff --git a/backend/src/monarch_py/implementations/solr/solr_implementation.py b/backend/src/monarch_py/implementations/solr/solr_implementation.py index 852929b09..b421a053a 100644 --- a/backend/src/monarch_py/implementations/solr/solr_implementation.py +++ b/backend/src/monarch_py/implementations/solr/solr_implementation.py @@ -289,12 +289,12 @@ def get_associations( associations = parse_associations(query_result, compact, offset, limit) return associations - def get_histopheno(self, subject_closure: Optional[str] = None) -> HistoPheno: + def get_histopheno(self, subject: Optional[str] = None) -> HistoPheno: """Get histopheno counts for a given subject_closure""" solr = SolrService(base_url=self.base_url, core=core.ASSOCIATION) - query = build_histopheno_query(subject_closure) + query = build_histopheno_query(subject) query_result = solr.query(query) - histopheno = parse_histopheno(query_result, subject_closure) + histopheno = parse_histopheno(query_result, subject) return histopheno def get_multi_entity_associations( 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 36ee1852c..730b25bd9 100644 --- a/backend/src/monarch_py/implementations/solr/solr_query_utils.py +++ b/backend/src/monarch_py/implementations/solr/solr_query_utils.py @@ -115,9 +115,9 @@ def build_association_counts_query(entity: str) -> SolrQuery: return query -def build_histopheno_query(subject_closure: str) -> SolrQuery: +def build_histopheno_query(subject: str) -> SolrQuery: query = build_association_query( - subject_closure=subject_closure, + subject=[subject], offset=0, limit=0, ) diff --git a/backend/tests/fixtures/association_counts_response.py b/backend/tests/fixtures/association_counts_response.py index fe99032cf..626b41014 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": 0, "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 3727db41a..c50cdccec 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": 1, + "QTime": 0, "params": { "mm": "100%", "q": "*:*", diff --git a/backend/tests/fixtures/histopheno.py b/backend/tests/fixtures/histopheno.py index 238753327..29853cd67 100644 --- a/backend/tests/fixtures/histopheno.py +++ b/backend/tests/fixtures/histopheno.py @@ -6,25 +6,25 @@ def histopheno(): return { "id": "MONDO:0020121", "items": [ - {"label": "musculature", "count": 1677, "id": "HP:0003011"}, - {"label": "nervous_system", "count": 1071, "id": "HP:0000707"}, - {"label": "head_neck", "count": 577, "id": "HP:0000152"}, - {"label": "skeletal_system", "count": 471, "id": "HP:0000924"}, - {"label": "eye", "count": 287, "id": "HP:0000478"}, + {"label": "musculature", "count": 1677, "id": "UPHENO:0002816"}, + {"label": "nervous_system", "count": 1071, "id": "UPHENO:0004523"}, + {"label": "head_neck", "count": 577, "id": "UPHENO:0002764"}, + {"label": "skeletal_system", "count": 471, "id": "UPHENO:0002964"}, + {"label": "eye", "count": 287, "id": "UPHENO:0003020"}, {"label": "metabolism_homeostasis", "count": 213, "id": "HP:0001939"}, - {"label": "cardiovascular_system", "count": 177, "id": "HP:0001626"}, - {"label": "blood", "count": 175, "id": "HP:0001871"}, - {"label": "connective_tissue", "count": 161, "id": "HP:0003549"}, - {"label": "respiratory", "count": 150, "id": "HP:0002086"}, + {"label": "cardiovascular_system", "count": 177, "id": "UPHENO:0080362"}, + {"label": "blood", "count": 175, "id": "UPHENO:0004459"}, + {"label": "connective_tissue", "count": 161, "id": "UPHENO:0002712"}, + {"label": "respiratory", "count": 150, "id": "UPHENO:0004536"}, {"label": "neoplasm", "count": 148, "id": "HP:0002664"}, - {"label": "digestive_system", "count": 142, "id": "HP:0025031"}, - {"label": "integument", "count": 47, "id": "HP:0001574"}, - {"label": "genitourinary_system", "count": 44, "id": "HP:0000119"}, - {"label": "growth", "count": 32, "id": "HP:0001507"}, + {"label": "digestive_system", "count": 142, "id": "UPHENO:0002833"}, + {"label": "integument", "count": 47, "id": "UPHENO:0002635"}, + {"label": "genitourinary_system", "count": 44, "id": "UPHENO:0002642"}, + {"label": "growth", "count": 32, "id": "UPHENO:0049874"}, {"label": "ear", "count": 28, "id": "HP:0000598"}, - {"label": "endocrine", "count": 25, "id": "HP:0000818"}, - {"label": "immune_system", "count": 22, "id": "HP:0002715"}, - {"label": "prenatal_or_birth", "count": 21, "id": "HP:0001197"}, - {"label": "breast", "count": 1, "id": "HP:0000769"}, + {"label": "endocrine", "count": 25, "id": "UPHENO:0003116"}, + {"label": "immune_system", "count": 22, "id": "UPHENO:0002948"}, + {"label": "prenatal_or_birth", "count": 21, "id": "UPHENO:0075949"}, + {"label": "breast", "count": 1, "id": "UPHENO:0003013"}, ], } diff --git a/backend/tests/fixtures/histopheno_query.py b/backend/tests/fixtures/histopheno_query.py index 0bb065bde..c11db3a51 100644 --- a/backend/tests/fixtures/histopheno_query.py +++ b/backend/tests/fixtures/histopheno_query.py @@ -11,28 +11,28 @@ def histopheno_query(): "facet_min_count": 1, "facet_fields": [], "facet_queries": [ - 'object_closure:"HP:0000924"', - 'object_closure:"HP:0000707"', - 'object_closure:"HP:0000152"', - 'object_closure:"HP:0001574"', - 'object_closure:"HP:0000478"', - 'object_closure:"HP:0001626"', + 'object_closure:"UPHENO:0002964"', + 'object_closure:"UPHENO:0004523"', + 'object_closure:"UPHENO:0002764"', + 'object_closure:"UPHENO:0002635"', + 'object_closure:"UPHENO:0003020"', + 'object_closure:"UPHENO:0080362"', 'object_closure:"HP:0001939"', - 'object_closure:"HP:0000119"', - 'object_closure:"HP:0025031"', + 'object_closure:"UPHENO:0002642"', + 'object_closure:"UPHENO:0002833"', 'object_closure:"HP:0002664"', - 'object_closure:"HP:0001871"', - 'object_closure:"HP:0002715"', - 'object_closure:"HP:0000818"', - 'object_closure:"HP:0003011"', - 'object_closure:"HP:0002086"', + 'object_closure:"UPHENO:0004459"', + 'object_closure:"UPHENO:0002948"', + 'object_closure:"UPHENO:0003116"', + 'object_closure:"UPHENO:0002816"', + 'object_closure:"UPHENO:0004536"', 'object_closure:"HP:0000598"', - 'object_closure:"HP:0003549"', - 'object_closure:"HP:0001197"', - 'object_closure:"HP:0001507"', - 'object_closure:"HP:0000769"', + 'object_closure:"UPHENO:0002712"', + 'object_closure:"UPHENO:0075949"', + 'object_closure:"UPHENO:0049874"', + 'object_closure:"UPHENO:0003013"', ], - "filter_queries": ["subject_closure:MONDO\\:0020121"], + "filter_queries": ['subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121"'], "query_fields": None, "def_type": "edismax", "q_op": "AND", diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py index 10605bbd1..945bae359 100644 --- a/backend/tests/fixtures/histopheno_response.py +++ b/backend/tests/fixtures/histopheno_response.py @@ -8,26 +8,26 @@ def histopheno_response(): "QTime": 1, "params": { "facet.query": [ - 'object_closure:"HP:0000924"', - 'object_closure:"HP:0000707"', - 'object_closure:"HP:0000152"', - 'object_closure:"HP:0001574"', - 'object_closure:"HP:0000478"', - 'object_closure:"HP:0001626"', + 'object_closure:"UPHENO:0002964"', + 'object_closure:"UPHENO:0004523"', + 'object_closure:"UPHENO:0002764"', + 'object_closure:"UPHENO:0002635"', + 'object_closure:"UPHENO:0003020"', + 'object_closure:"UPHENO:0080362"', 'object_closure:"HP:0001939"', - 'object_closure:"HP:0000119"', - 'object_closure:"HP:0025031"', + 'object_closure:"UPHENO:0002642"', + 'object_closure:"UPHENO:0002833"', 'object_closure:"HP:0002664"', - 'object_closure:"HP:0001871"', - 'object_closure:"HP:0002715"', - 'object_closure:"HP:0000818"', - 'object_closure:"HP:0003011"', - 'object_closure:"HP:0002086"', + 'object_closure:"UPHENO:0004459"', + 'object_closure:"UPHENO:0002948"', + 'object_closure:"UPHENO:0003116"', + 'object_closure:"UPHENO:0002816"', + 'object_closure:"UPHENO:0004536"', 'object_closure:"HP:0000598"', - 'object_closure:"HP:0003549"', - 'object_closure:"HP:0001197"', - 'object_closure:"HP:0001507"', - 'object_closure:"HP:0000769"', + 'object_closure:"UPHENO:0002712"', + 'object_closure:"UPHENO:0075949"', + 'object_closure:"UPHENO:0049874"', + 'object_closure:"UPHENO:0003013"', ], "mm": "100%", "q": "*:*", @@ -35,7 +35,7 @@ def histopheno_response(): "facet_min_count": "1", "start": "0", "q.op": "AND", - "fq": "subject_closure:MONDO\\:0020121", + "fq": 'subject:"MONDO:0020121" OR subject_closure:"MONDO:0020121"', "rows": "0", "facet": "true", }, @@ -44,26 +44,26 @@ def histopheno_response(): "facet_counts": { "facet_fields": {}, "facet_queries": { - 'object_closure:"HP:0000924"': 471, - 'object_closure:"HP:0000707"': 1071, - 'object_closure:"HP:0000152"': 577, - 'object_closure:"HP:0001574"': 47, - 'object_closure:"HP:0000478"': 287, - 'object_closure:"HP:0001626"': 177, + 'object_closure:"UPHENO:0002964"': 471, + 'object_closure:"UPHENO:0004523"': 1071, + 'object_closure:"UPHENO:0002764"': 577, + 'object_closure:"UPHENO:0002635"': 47, + 'object_closure:"UPHENO:0003020"': 287, + 'object_closure:"UPHENO:0080362"': 177, 'object_closure:"HP:0001939"': 213, - 'object_closure:"HP:0000119"': 44, - 'object_closure:"HP:0025031"': 142, + 'object_closure:"UPHENO:0002642"': 44, + 'object_closure:"UPHENO:0002833"': 142, 'object_closure:"HP:0002664"': 148, - 'object_closure:"HP:0001871"': 175, - 'object_closure:"HP:0002715"': 22, - 'object_closure:"HP:0000818"': 25, - 'object_closure:"HP:0003011"': 1677, - 'object_closure:"HP:0002086"': 150, + 'object_closure:"UPHENO:0004459"': 175, + 'object_closure:"UPHENO:0002948"': 22, + 'object_closure:"UPHENO:0003116"': 25, + 'object_closure:"UPHENO:0002816"': 1677, + 'object_closure:"UPHENO:0004536"': 150, 'object_closure:"HP:0000598"': 28, - 'object_closure:"HP:0003549"': 161, - 'object_closure:"HP:0001197"': 21, - 'object_closure:"HP:0001507"': 32, - 'object_closure:"HP:0000769"': 1, + 'object_closure:"UPHENO:0002712"': 161, + 'object_closure:"UPHENO:0075949"': 21, + 'object_closure:"UPHENO:0049874"': 32, + 'object_closure:"UPHENO:0003013"': 1, }, }, } diff --git a/backend/tests/fixtures/search_response.py b/backend/tests/fixtures/search_response.py index 3586bd0dc..08aa81c6b 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": 2, + "QTime": 0, "params": { "mm": "100%", "q": "fanconi", diff --git a/backend/tests/integration/test_solr_histopheno.py b/backend/tests/integration/test_solr_histopheno.py index 767e05b7c..c42fa71dd 100644 --- a/backend/tests/integration/test_solr_histopheno.py +++ b/backend/tests/integration/test_solr_histopheno.py @@ -15,4 +15,4 @@ def test_histopheno(): for k in hp.items: total += k.count - assert hp.items[0].id == "HP:0003011" + assert hp.items[0].id == "UPHENO:0002816" diff --git a/backend/tests/unit/test_solr_queries.py b/backend/tests/unit/test_solr_queries.py index 018447a62..3e10ce785 100644 --- a/backend/tests/unit/test_solr_queries.py +++ b/backend/tests/unit/test_solr_queries.py @@ -14,7 +14,8 @@ build_search_query, obsolete_unboost, entity_predicate_boost, - category_boost, blank_search_boost, + category_boost, + blank_search_boost, ) from monarch_py.utils.utils import compare_dicts, dict_diff @@ -164,5 +165,4 @@ def test_blank_search_boost(): boost = blank_search_boost() assert boost.startswith("product(") assert boost.endswith(")") - assert "if(termfreq(id,\"MONDO:0007523\"),12,1)" in boost - + assert 'if(termfreq(id,"MONDO:0007523"),12,1)' in boost diff --git a/frontend/fixtures/histopheno.json b/frontend/fixtures/histopheno.json index 64e52a93e..e41c04d2d 100644 --- a/frontend/fixtures/histopheno.json +++ b/frontend/fixtures/histopheno.json @@ -4,27 +4,27 @@ { "label": "musculature", "count": 1677, - "id": "HP:0003011" + "id": "UPHENO:0002816" }, { "label": "nervous_system", "count": 1071, - "id": "HP:0000707" + "id": "UPHENO:0004523" }, { "label": "head_neck", "count": 577, - "id": "HP:0000152" + "id": "UPHENO:0002764" }, { "label": "skeletal_system", "count": 471, - "id": "HP:0000924" + "id": "UPHENO:0002964" }, { "label": "eye", "count": 287, - "id": "HP:0000478" + "id": "UPHENO:0003020" }, { "label": "metabolism_homeostasis", @@ -34,22 +34,22 @@ { "label": "cardiovascular_system", "count": 177, - "id": "HP:0001626" + "id": "UPHENO:0080362" }, { "label": "blood", "count": 175, - "id": "HP:0001871" + "id": "UPHENO:0004459" }, { "label": "connective_tissue", "count": 161, - "id": "HP:0003549" + "id": "UPHENO:0002712" }, { "label": "respiratory", "count": 150, - "id": "HP:0002086" + "id": "UPHENO:0004536" }, { "label": "neoplasm", @@ -59,22 +59,22 @@ { "label": "digestive_system", "count": 142, - "id": "HP:0025031" + "id": "UPHENO:0002833" }, { "label": "integument", "count": 47, - "id": "HP:0001574" + "id": "UPHENO:0002635" }, { "label": "genitourinary_system", "count": 44, - "id": "HP:0000119" + "id": "UPHENO:0002642" }, { "label": "growth", "count": 32, - "id": "HP:0001507" + "id": "UPHENO:0049874" }, { "label": "ear", @@ -84,22 +84,22 @@ { "label": "endocrine", "count": 25, - "id": "HP:0000818" + "id": "UPHENO:0003116" }, { "label": "immune_system", "count": 22, - "id": "HP:0002715" + "id": "UPHENO:0002948" }, { "label": "prenatal_or_birth", "count": 21, - "id": "HP:0001197" + "id": "UPHENO:0075949" }, { "label": "breast", "count": 1, - "id": "HP:0000769" + "id": "UPHENO:0003013" } ] } diff --git a/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json index 33edf866b..ec68ccf92 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 (MPO)" - }, "MP:0002169": { "id": "MP:0002169", "label": "no abnormal phenotype detected (MPO)" + }, + "MP:0010771": { + "id": "MP:0010771", + "label": "integument phenotype (MPO)" } }, "object_termset": { @@ -77,8 +77,8 @@ "HP:0004325": { "match_source": "HP:0004325", "match_source_label": "Decreased body weight (HPO)", - "match_target": "MP:0010771", - "match_target_label": "integument phenotype (MPO)", + "match_target": "MP:0002169", + "match_target_label": "no abnormal phenotype detected (MPO)", "score": 1.5540019332516637, "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": 1.5540019332516637, - "jaccard_similarity": 0.24, + "jaccard_similarity": 0.23076923076923078, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.61070489107293 + "phenodigm_score": 0.5988454147360435 }, "score_metric": "ancestor_information_content" } diff --git a/frontend/fixtures/phenotype-explorer-multi-compare.json b/frontend/fixtures/phenotype-explorer-multi-compare.json index cd464946e..0c5dbb527 100644 --- a/frontend/fixtures/phenotype-explorer-multi-compare.json +++ b/frontend/fixtures/phenotype-explorer-multi-compare.json @@ -22,45 +22,45 @@ "has_phenotype_closure_label": [], "has_phenotype_count": null }, - "score": 0.5499139182472517, + "score": 0.5499139182472516, "similarity": { "subject_termset": { - "HP:0004944": { - "id": "HP:0004944", - "label": "Dilatation of the cerebral artery (HPO)" - }, - "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" }, - "HP:0012450": { - "id": "HP:0012450", - "label": "Chronic constipation (HPO)" + "HP:0002616": { + "id": "HP:0002616", + "label": "Aortic root aneurysm (HPO)" }, "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux (HPO)" }, + "HP:0012450": { + "id": "HP:0012450", + "label": "Chronic constipation (HPO)" + }, "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" }, - "HP:0002616": { - "id": "HP:0002616", - "label": "Aortic root aneurysm (HPO)" + "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, + "HP:0004944": { + "id": "HP:0004944", + "label": "Dilatation of the cerebral artery (HPO)" }, - "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" } + "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" } }, "object_termset": { - "HP:0002108": { - "id": "HP:0002108", - "label": "Spontaneous pneumothorax (HPO)" - }, - "HP:0000545": { "id": "HP:0000545", "label": "Myopia (HPO)" }, - "HP:0100785": { "id": "HP:0100785", "label": "Insomnia (HPO)" }, - "HP:0000023": { "id": "HP:0000023", "label": "Inguinal hernia (HPO)" }, + "HP:0000268": { "id": "HP:0000268", "label": "Dolichocephaly (HPO)" }, "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm (HPO)" }, "HP:0000767": { "id": "HP:0000767", "label": "Pectus excavatum (HPO)" }, - "HP:0000268": { "id": "HP:0000268", "label": "Dolichocephaly (HPO)" }, + "HP:0000545": { "id": "HP:0000545", "label": "Myopia (HPO)" }, + "HP:0000023": { "id": "HP:0000023", "label": "Inguinal hernia (HPO)" }, "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, - "HP:0000490": { "id": "HP:0000490", "label": "Deeply set eye (HPO)" } + "HP:0000490": { "id": "HP:0000490", "label": "Deeply set eye (HPO)" }, + "HP:0100785": { "id": "HP:0100785", "label": "Insomnia (HPO)" }, + "HP:0002108": { + "id": "HP:0002108", + "label": "Spontaneous pneumothorax (HPO)" + } }, "subject_best_matches": { "HP:0001533": { @@ -264,16 +264,16 @@ "HP:0000023": { "match_source": "HP:0000023", "match_source_label": "Inguinal hernia (HPO)", - "match_target": "HP:0002020", - "match_target_label": "Gastroesophageal reflux (HPO)", - "score": 0.36363636363636365, + "match_target": "HP:0012450", + "match_target_label": "Chronic constipation (HPO)", + "score": 0.4, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0000023", "subject_label": null, "subject_source": null, - "object_id": "HP:0002020", + "object_id": "HP:0012450", "object_label": null, "object_source": null, "ancestor_id": "HP:0025031", @@ -282,10 +282,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.826350815132431, - "jaccard_similarity": 0.36363636363636365, + "jaccard_similarity": 0.4, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.686993109338994 + "phenodigm_score": 1.769333299876813 }, "score_metric": "jaccard_similarity" }, @@ -432,16 +432,16 @@ "HP:0002108": { "match_source": "HP:0002108", "match_source_label": "Spontaneous pneumothorax (HPO)", - "match_target": "HP:0002020", - "match_target_label": "Gastroesophageal reflux (HPO)", - "score": 0.2926829268292683, + "match_target": "HP:0004944", + "match_target_label": "Dilatation of the cerebral artery (HPO)", + "score": 0.2807017543859649, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0002108", "subject_label": null, "subject_source": null, - "object_id": "HP:0002020", + "object_id": "HP:0004944", "object_label": null, "object_source": null, "ancestor_id": "HP:0000118", @@ -450,10 +450,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 4.118848568918744, - "jaccard_similarity": 0.2926829268292683, + "jaccard_similarity": 0.2807017543859649, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.09796022437868 + "phenodigm_score": 1.0752525374746216 }, "score_metric": "jaccard_similarity" }, @@ -514,7 +514,7 @@ "score_metric": "jaccard_similarity" } }, - "average_score": 0.5499139182472517, + "average_score": 0.5499139182472516, "best_score": 1.0, "metric": "JaccardSimilarity" } @@ -545,66 +545,66 @@ "score": 0.83497558824921, "similarity": { "subject_termset": { - "HP:0002616": { - "id": "HP:0002616", - "label": "Aortic root aneurysm (HPO)" - }, - "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" }, - "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation (HPO)" }, - "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" }, "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux (HPO)" }, - "HP:0004944": { - "id": "HP:0004944", - "label": "Dilatation of the cerebral artery (HPO)" - } - }, - "object_termset": { "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm (HPO)" }, + "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" }, "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" }, "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, - "HP:0001278": { - "id": "HP:0001278", - "label": "Orthostatic hypotension (HPO)" - }, - "HP:0003010": { - "id": "HP:0003010", - "label": "Prolonged bleeding time (HPO)" - }, + "HP:0004944": { + "id": "HP:0004944", + "label": "Dilatation of the cerebral artery (HPO)" + } + }, + "object_termset": { + "HP:0003394": { "id": "HP:0003394", "label": "Muscle spasm (HPO)" }, "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation (HPO)" }, - "HP:0002829": { "id": "HP:0002829", "label": "Arthralgia (HPO)" }, - "HP:0003394": { "id": "HP:0003394", "label": "Muscle spasm (HPO)" }, - "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" }, "HP:0002020": { "id": "HP:0002020", "label": "Gastroesophageal reflux (HPO)" }, + "HP:0002829": { "id": "HP:0002829", "label": "Arthralgia (HPO)" }, + "HP:0002999": { + "id": "HP:0002999", + "label": "Patellar dislocation (HPO)" + }, + "HP:0002827": { "id": "HP:0002827", "label": "Hip dislocation (HPO)" }, + "HP:0002616": { + "id": "HP:0002616", + "label": "Aortic root aneurysm (HPO)" + }, + "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" }, "HP:0003771": { "id": "HP:0003771", "label": "Pulp calcification (HPO)" }, + "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" }, + "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, + "HP:0003010": { + "id": "HP:0003010", + "label": "Prolonged bleeding time (HPO)" + }, + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" }, "HP:0004944": { "id": "HP:0004944", "label": "Dilatation of the cerebral artery (HPO)" }, - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" }, - "HP:0002999": { - "id": "HP:0002999", - "label": "Patellar dislocation (HPO)" - }, - "HP:0002827": { "id": "HP:0002827", "label": "Hip dislocation (HPO)" } + "HP:0001278": { + "id": "HP:0001278", + "label": "Orthostatic hypotension (HPO)" + } }, "subject_best_matches": { "HP:0001533": { @@ -808,16 +808,16 @@ "HP:0001278": { "match_source": "HP:0001278", "match_source_label": "Orthostatic hypotension (HPO)", - "match_target": "HP:0002616", - "match_target_label": "Aortic root aneurysm (HPO)", - "score": 0.3076923076923077, + "match_target": "HP:0004944", + "match_target_label": "Dilatation of the cerebral artery (HPO)", + "score": 0.2903225806451613, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0001278", "subject_label": null, "subject_source": null, - "object_id": "HP:0002616", + "object_id": "HP:0004944", "object_label": null, "object_source": null, "ancestor_id": "HP:0002597", @@ -826,10 +826,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 8.38058018831398, - "jaccard_similarity": 0.3076923076923077, + "jaccard_similarity": 0.2903225806451613, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.6058144531491685 + "phenodigm_score": 1.55983065349256 }, "score_metric": "jaccard_similarity" }, @@ -976,16 +976,16 @@ "HP:0002829": { "match_source": "HP:0002829", "match_source_label": "Arthralgia (HPO)", - "match_target": "HP:0012450", - "match_target_label": "Chronic constipation (HPO)", - "score": 0.38461538461538464, + "match_target": "HP:0001763", + "match_target_label": "Pes planus (HPO)", + "score": 0.23809523809523808, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0002829", "subject_label": null, "subject_source": null, - "object_id": "HP:0012450", + "object_id": "HP:0001763", "object_label": null, "object_source": null, "ancestor_id": "HP:0000118", @@ -994,10 +994,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 4.118848568918744, - "jaccard_similarity": 0.38461538461538464, + "jaccard_similarity": 0.23809523809523808, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.2586391565922337 + "phenodigm_score": 0.990291992644058 }, "score_metric": "jaccard_similarity" }, @@ -1032,16 +1032,16 @@ "HP:0003010": { "match_source": "HP:0003010", "match_source_label": "Prolonged bleeding time (HPO)", - "match_target": "HP:0002616", - "match_target_label": "Aortic root aneurysm (HPO)", - "score": 0.28205128205128205, + "match_target": "HP:0004944", + "match_target_label": "Dilatation of the cerebral artery (HPO)", + "score": 0.21568627450980393, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0003010", "subject_label": null, "subject_source": null, - "object_id": "HP:0002616", + "object_id": "HP:0004944", "object_label": null, "object_source": null, "ancestor_id": "HP:0000118", @@ -1050,10 +1050,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 4.118848568918744, - "jaccard_similarity": 0.28205128205128205, + "jaccard_similarity": 0.21568627450980393, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.077834179936144 + "phenodigm_score": 0.9425386480670812 }, "score_metric": "jaccard_similarity" }, @@ -1172,16 +1172,16 @@ "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue (HPO)", - "match_target": "HP:0010749", - "match_target_label": "Blepharochalasis (HPO)", - "score": 0.18867924528301888, + "match_target": "HP:0001533", + "match_target_label": "Slender build (HPO)", + "score": 0.23809523809523808, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "HP:0010749", + "object_id": "HP:0001533", "object_label": null, "object_source": null, "ancestor_id": "HP:0000118", @@ -1190,10 +1190,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 4.118848568918744, - "jaccard_similarity": 0.18867924528301888, + "jaccard_similarity": 0.23809523809523808, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8815561464924574 + "phenodigm_score": 0.990291992644058 }, "score_metric": "jaccard_similarity" }, @@ -1257,82 +1257,82 @@ "score": 0.5309539844387191, "similarity": { "subject_termset": { - "HP:0002020": { - "id": "HP:0002020", - "label": "Gastroesophageal reflux (HPO)" + "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, + "HP:0002616": { + "id": "HP:0002616", + "label": "Aortic root aneurysm (HPO)" }, "HP:0004944": { "id": "HP:0004944", "label": "Dilatation of the cerebral artery (HPO)" }, + "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" }, "HP:0012450": { "id": "HP:0012450", "label": "Chronic constipation (HPO)" }, + "HP:0002020": { + "id": "HP:0002020", + "label": "Gastroesophageal reflux (HPO)" + }, + "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" } + }, + "object_termset": { "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, "HP:0002616": { "id": "HP:0002616", "label": "Aortic root aneurysm (HPO)" }, - "HP:0010749": { "id": "HP:0010749", "label": "Blepharochalasis (HPO)" }, - "HP:0001533": { "id": "HP:0001533", "label": "Slender build (HPO)" } - }, - "object_termset": { - "HP:0003179": { - "id": "HP:0003179", - "label": "Protrusio acetabuli (HPO)" + "HP:0012432": { "id": "HP:0012432", "label": "Chronic fatigue (HPO)" }, + "HP:0000023": { "id": "HP:0000023", "label": "Inguinal hernia (HPO)" }, + "HP:0000268": { "id": "HP:0000268", "label": "Dolichocephaly (HPO)" }, + "HP:0100785": { "id": "HP:0100785", "label": "Insomnia (HPO)" }, + "HP:0000545": { "id": "HP:0000545", "label": "Myopia (HPO)" }, + "HP:0005059": { + "id": "HP:0005059", + "label": "Arthralgia/arthritis (HPO)" }, - "HP:0004970": { - "id": "HP:0004970", - "label": "Ascending tubular aorta aneurysm (HPO)" + "HP:0001659": { + "id": "HP:0001659", + "label": "Aortic regurgitation (HPO)" }, - "HP:0002705": { - "id": "HP:0002705", - "label": "High, narrow palate (HPO)" + "HP:0001704": { + "id": "HP:0001704", + "label": "Tricuspid valve prolapse (HPO)" + }, + "HP:0001634": { + "id": "HP:0001634", + "label": "Mitral valve prolapse (HPO)" }, - "HP:0000767": { "id": "HP:0000767", "label": "Pectus excavatum (HPO)" }, "HP:0007800": { "id": "HP:0007800", "label": "Increased axial length of the globe (HPO)" }, - "HP:0002108": { - "id": "HP:0002108", - "label": "Spontaneous pneumothorax (HPO)" - }, - "HP:0000490": { "id": "HP:0000490", "label": "Deeply set eye (HPO)" }, "HP:0002360": { "id": "HP:0002360", "label": "Sleep disturbance (HPO)" }, - "HP:0001763": { "id": "HP:0001763", "label": "Pes planus (HPO)" }, - "HP:0001659": { - "id": "HP:0001659", - "label": "Aortic regurgitation (HPO)" + "HP:0004970": { + "id": "HP:0004970", + "label": "Ascending tubular aorta aneurysm (HPO)" }, - "HP:0005059": { - "id": "HP:0005059", - "label": "Arthralgia/arthritis (HPO)" + "HP:0000490": { "id": "HP:0000490", "label": "Deeply set eye (HPO)" }, + "HP:0002705": { + "id": "HP:0002705", + "label": "High, narrow palate (HPO)" + }, + "HP:0000767": { "id": "HP:0000767", "label": "Pectus excavatum (HPO)" }, + "HP:0003179": { + "id": "HP:0003179", + "label": "Protrusio acetabuli (HPO)" }, - "HP:0012432": { "id": "HP:0012432", "label": "Chronic fatigue (HPO)" }, - "HP:0000023": { "id": "HP:0000023", "label": "Inguinal hernia (HPO)" }, "HP:0001653": { "id": "HP:0001653", "label": "Mitral regurgitation (HPO)" }, - "HP:0000268": { "id": "HP:0000268", "label": "Dolichocephaly (HPO)" }, - "HP:0002616": { - "id": "HP:0002616", - "label": "Aortic root aneurysm (HPO)" - }, - "HP:0100785": { "id": "HP:0100785", "label": "Insomnia (HPO)" }, - "HP:0001634": { - "id": "HP:0001634", - "label": "Mitral valve prolapse (HPO)" - }, - "HP:0000545": { "id": "HP:0000545", "label": "Myopia (HPO)" }, - "HP:0001704": { - "id": "HP:0001704", - "label": "Tricuspid valve prolapse (HPO)" + "HP:0002108": { + "id": "HP:0002108", + "label": "Spontaneous pneumothorax (HPO)" } }, "subject_best_matches": { @@ -1395,16 +1395,16 @@ "HP:0002020": { "match_source": "HP:0002020", "match_source_label": "Gastroesophageal reflux (HPO)", - "match_target": "HP:0000023", - "match_target_label": "Inguinal hernia (HPO)", - "score": 0.36363636363636365, + "match_target": "HP:0002705", + "match_target_label": "High, narrow palate (HPO)", + "score": 0.24615384615384617, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0002020", "subject_label": null, "subject_source": null, - "object_id": "HP:0000023", + "object_id": "HP:0002705", "object_label": null, "object_source": null, "ancestor_id": "HP:0025031", @@ -1413,10 +1413,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.826350815132431, - "jaccard_similarity": 0.36363636363636365, + "jaccard_similarity": 0.24615384615384617, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.686993109338994 + "phenodigm_score": 1.3879792341725206 }, "score_metric": "jaccard_similarity" }, @@ -1451,8 +1451,8 @@ "HP:0004944": { "match_source": "HP:0004944", "match_source_label": "Dilatation of the cerebral artery (HPO)", - "match_target": "HP:0004970", - "match_target_label": "Ascending tubular aorta aneurysm (HPO)", + "match_target": "HP:0002616", + "match_target_label": "Aortic root aneurysm (HPO)", "score": 0.5185185185185185, "match_subsumer": null, "match_subsumer_label": null, @@ -1460,7 +1460,7 @@ "subject_id": "HP:0004944", "subject_label": null, "subject_source": null, - "object_id": "HP:0004970", + "object_id": "HP:0002616", "object_label": null, "object_source": null, "ancestor_id": "HP:0002617", @@ -1507,16 +1507,16 @@ "HP:0012450": { "match_source": "HP:0012450", "match_source_label": "Chronic constipation (HPO)", - "match_target": "HP:0000023", - "match_target_label": "Inguinal hernia (HPO)", - "score": 0.4, + "match_target": "HP:0002705", + "match_target_label": "High, narrow palate (HPO)", + "score": 0.26229508196721313, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0012450", "subject_label": null, "subject_source": null, - "object_id": "HP:0000023", + "object_id": "HP:0002705", "object_label": null, "object_source": null, "ancestor_id": "HP:0025031", @@ -1525,10 +1525,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.826350815132431, - "jaccard_similarity": 0.4, + "jaccard_similarity": 0.26229508196721313, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.769333299876813 + "phenodigm_score": 1.432764226437597 }, "score_metric": "jaccard_similarity" } @@ -1537,16 +1537,16 @@ "HP:0000023": { "match_source": "HP:0000023", "match_source_label": "Inguinal hernia (HPO)", - "match_target": "HP:0012450", - "match_target_label": "Chronic constipation (HPO)", - "score": 0.4, + "match_target": "HP:0002020", + "match_target_label": "Gastroesophageal reflux (HPO)", + "score": 0.36363636363636365, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0000023", "subject_label": null, "subject_source": null, - "object_id": "HP:0012450", + "object_id": "HP:0002020", "object_label": null, "object_source": null, "ancestor_id": "HP:0025031", @@ -1555,10 +1555,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.826350815132431, - "jaccard_similarity": 0.4, + "jaccard_similarity": 0.36363636363636365, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.769333299876813 + "phenodigm_score": 1.686993109338994 }, "score_metric": "jaccard_similarity" }, @@ -1705,16 +1705,16 @@ "HP:0001653": { "match_source": "HP:0001653", "match_source_label": "Mitral regurgitation (HPO)", - "match_target": "HP:0002616", - "match_target_label": "Aortic root aneurysm (HPO)", - "score": 0.30434782608695654, + "match_target": "HP:0004944", + "match_target_label": "Dilatation of the cerebral artery (HPO)", + "score": 0.2413793103448276, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0001653", "subject_label": null, "subject_source": null, - "object_id": "HP:0002616", + "object_id": "HP:0004944", "object_label": null, "object_source": null, "ancestor_id": "HP:0001626", @@ -1723,26 +1723,26 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.652086110215225, - "jaccard_similarity": 0.30434782608695654, + "jaccard_similarity": 0.2413793103448276, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.5260720076962944 + "phenodigm_score": 1.3590641147432985 }, "score_metric": "jaccard_similarity" }, "HP:0001659": { "match_source": "HP:0001659", "match_source_label": "Aortic regurgitation (HPO)", - "match_target": "HP:0004944", - "match_target_label": "Dilatation of the cerebral artery (HPO)", - "score": 0.25, + "match_target": "HP:0002616", + "match_target_label": "Aortic root aneurysm (HPO)", + "score": 0.3181818181818182, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0001659", "subject_label": null, "subject_source": null, - "object_id": "HP:0004944", + "object_id": "HP:0002616", "object_label": null, "object_source": null, "ancestor_id": "HP:0001626", @@ -1751,10 +1751,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 7.652086110215225, - "jaccard_similarity": 0.25, + "jaccard_similarity": 0.3181818181818182, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.3831202144259935 + "phenodigm_score": 1.560370043109043 }, "score_metric": "jaccard_similarity" }, @@ -1817,16 +1817,16 @@ "HP:0002108": { "match_source": "HP:0002108", "match_source_label": "Spontaneous pneumothorax (HPO)", - "match_target": "HP:0001533", - "match_target_label": "Slender build (HPO)", - "score": 0.32, + "match_target": "HP:0002020", + "match_target_label": "Gastroesophageal reflux (HPO)", + "score": 0.2926829268292683, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0002108", "subject_label": null, "subject_source": null, - "object_id": "HP:0001533", + "object_id": "HP:0002020", "object_label": null, "object_source": null, "ancestor_id": "HP:0000118", @@ -1835,10 +1835,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 4.118848568918744, - "jaccard_similarity": 0.32, + "jaccard_similarity": 0.2926829268292683, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.1480555483311763 + "phenodigm_score": 1.09796022437868 }, "score_metric": "jaccard_similarity" }, @@ -2041,16 +2041,16 @@ "HP:0012432": { "match_source": "HP:0012432", "match_source_label": "Chronic fatigue (HPO)", - "match_target": "HP:0001533", - "match_target_label": "Slender build (HPO)", - "score": 0.23255813953488372, + "match_target": "HP:0002020", + "match_target_label": "Gastroesophageal reflux (HPO)", + "score": 0.3333333333333333, "match_subsumer": null, "match_subsumer_label": null, "similarity": { "subject_id": "HP:0012432", "subject_label": null, "subject_source": null, - "object_id": "HP:0001533", + "object_id": "HP:0002020", "object_label": null, "object_source": null, "ancestor_id": "HP:0000118", @@ -2059,10 +2059,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 4.118848568918744, - "jaccard_similarity": 0.23255813953488372, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.9787092316994161 + "phenodigm_score": 1.171729287409389 }, "score_metric": "jaccard_similarity" }, diff --git a/frontend/fixtures/phenotype-explorer-search.json b/frontend/fixtures/phenotype-explorer-search.json index 2767abf23..741fe95b5 100644 --- a/frontend/fixtures/phenotype-explorer-search.json +++ b/frontend/fixtures/phenotype-explorer-search.json @@ -250,8 +250,8 @@ } }, "object_termset": { - "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" }, - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" } + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" }, + "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" } }, "subject_best_matches": { "ZP:0018568": { @@ -315,8 +315,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea (HPO)", - "match_target": "ZP:0018568", - "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", + "match_target": "ZP:0018569", + "match_target_label": "myeloid cell development absent, abnormal (ZPO)", "score": 9.08524944639702, "match_subsumer": null, "match_subsumer_label": null, @@ -324,7 +324,7 @@ "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", @@ -333,10 +333,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.08524944639702, - "jaccard_similarity": 0.3333333333333333, + "jaccard_similarity": 0.34615384615384615, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.7402346054863809 + "phenodigm_score": 1.773384910034319 }, "score_metric": "ancestor_information_content" }, @@ -443,18 +443,18 @@ "score": 7.234842285670967, "similarity": { "subject_termset": { - "ZP:0018569": { - "id": "ZP:0018569", - "label": "myeloid cell development absent, abnormal (ZPO)" - }, "ZP:0018568": { "id": "ZP:0018568", "label": "primitive hemopoiesis absent, abnormal (ZPO)" + }, + "ZP:0018569": { + "id": "ZP:0018569", + "label": "myeloid cell development absent, abnormal (ZPO)" } }, "object_termset": { - "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" }, - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" } + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" }, + "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" } }, "subject_best_matches": { "ZP:0018568": { @@ -546,8 +546,8 @@ "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 1.6836208034928104, "match_subsumer": null, "match_subsumer_label": null, @@ -555,7 +555,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -564,10 +564,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6836208034928104, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.4444444444444444, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8901079388591847 + "phenodigm_score": 0.8650294287846346 }, "score_metric": "ancestor_information_content" } @@ -653,13 +653,13 @@ "score": 7.234842285670967, "similarity": { "subject_termset": { - "ZP:0018568": { - "id": "ZP:0018568", - "label": "primitive hemopoiesis absent, abnormal (ZPO)" - }, "ZP:0018569": { "id": "ZP:0018569", "label": "myeloid cell development absent, abnormal (ZPO)" + }, + "ZP:0018568": { + "id": "ZP:0018568", + "label": "primitive hemopoiesis absent, abnormal (ZPO)" } }, "object_termset": { @@ -756,8 +756,8 @@ "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue (HPO)", - "match_target": "ZP:0018568", - "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", + "match_target": "ZP:0018569", + "match_target_label": "myeloid cell development absent, abnormal (ZPO)", "score": 1.6836208034928104, "match_subsumer": null, "match_subsumer_label": null, @@ -765,7 +765,7 @@ "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", @@ -774,10 +774,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6836208034928104, - "jaccard_similarity": 0.4444444444444444, + "jaccard_similarity": 0.47058823529411764, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8650294287846346 + "phenodigm_score": 0.8901079388591847 }, "score_metric": "ancestor_information_content" } @@ -863,18 +863,18 @@ "score": 7.234842285670967, "similarity": { "subject_termset": { - "ZP:0018568": { - "id": "ZP:0018568", - "label": "primitive hemopoiesis absent, abnormal (ZPO)" - }, "ZP:0018569": { "id": "ZP:0018569", "label": "myeloid cell development absent, abnormal (ZPO)" + }, + "ZP:0018568": { + "id": "ZP:0018568", + "label": "primitive hemopoiesis absent, abnormal (ZPO)" } }, "object_termset": { - "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" }, - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" } + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" }, + "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" } }, "subject_best_matches": { "ZP:0018568": { @@ -938,8 +938,8 @@ "HP:0002104": { "match_source": "HP:0002104", "match_source_label": "Apnea (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 9.08524944639702, "match_subsumer": null, "match_subsumer_label": null, @@ -947,7 +947,7 @@ "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", @@ -956,18 +956,18 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 9.08524944639702, - "jaccard_similarity": 0.34615384615384615, + "jaccard_similarity": 0.3333333333333333, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 1.773384910034319 + "phenodigm_score": 1.7402346054863809 }, "score_metric": "ancestor_information_content" }, "HP:0012378": { "match_source": "HP:0012378", "match_source_label": "Fatigue (HPO)", - "match_target": "ZP:0018569", - "match_target_label": "myeloid cell development absent, abnormal (ZPO)", + "match_target": "ZP:0018568", + "match_target_label": "primitive hemopoiesis absent, abnormal (ZPO)", "score": 1.6836208034928104, "match_subsumer": null, "match_subsumer_label": null, @@ -975,7 +975,7 @@ "subject_id": "HP:0012378", "subject_label": null, "subject_source": null, - "object_id": "ZP:0018569", + "object_id": "ZP:0018568", "object_label": null, "object_source": null, "ancestor_id": "UPHENO:0001005", @@ -984,10 +984,10 @@ "object_information_content": null, "subject_information_content": null, "ancestor_information_content": 1.6836208034928104, - "jaccard_similarity": 0.47058823529411764, + "jaccard_similarity": 0.4444444444444444, "cosine_similarity": null, "dice_similarity": null, - "phenodigm_score": 0.8901079388591847 + "phenodigm_score": 0.8650294287846346 }, "score_metric": "ancestor_information_content" } @@ -1267,13 +1267,13 @@ "score": 5.384435124944915, "similarity": { "subject_termset": { - "ZP:0015039": { - "id": "ZP:0015039", - "label": "visual behavior absent, abnormal (ZPO)" - }, "ZP:0001841": { "id": "ZP:0001841", "label": "visual behavior quality, abnormal (ZPO)" + }, + "ZP:0015039": { + "id": "ZP:0015039", + "label": "visual behavior absent, abnormal (ZPO)" } }, "object_termset": { @@ -1676,8 +1676,8 @@ } }, "object_termset": { - "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" }, - "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" } + "HP:0002104": { "id": "HP:0002104", "label": "Apnea (HPO)" }, + "HP:0012378": { "id": "HP:0012378", "label": "Fatigue (HPO)" } }, "subject_best_matches": { "ZP:0003210": { diff --git a/frontend/src/pages/node/SectionVisualization.vue b/frontend/src/pages/node/SectionVisualization.vue index 6c9fe967e..c33ed0110 100644 --- a/frontend/src/pages/node/SectionVisualization.vue +++ b/frontend/src/pages/node/SectionVisualization.vue @@ -1,9 +1,13 @@ -