Manually change ts model scores to numbers (also updated to latest li…

…nkml, but it doesn't have the fix yet)
monarch-initiative · Nov 16, 2023 · a8d69ae · a8d69ae
1 parent cde1104
commit a8d69ae
Show file tree

Hide file tree

Showing 8 changed files with 45 additions and 52 deletions.
diff --git a/backend/poetry.lock b/backend/poetry.lock
diff --git a/backend/pyproject.toml b/backend/pyproject.toml
@@ -19,7 +19,7 @@ packages = [
 python = "^3.9"
 pydantic = "^1.10.2"
 curies = "<1"
-linkml = "^1.6.1"
+linkml = "^1.6.2"
 prefixmaps = "^0.1.7"
 
 requests = "^2.28.1"

diff --git a/backend/tests/fixtures/autocomplete_response.py b/backend/tests/fixtures/autocomplete_response.py
@@ -5,7 +5,7 @@
 def autocomplete_response():
     return {
         "responseHeader": {
-            "QTime": 1,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanc",

diff --git a/backend/tests/fixtures/histopheno_response.py b/backend/tests/fixtures/histopheno_response.py
@@ -5,7 +5,7 @@
 def histopheno_response():
     return {
         "responseHeader": {
-            "QTime": 4,
+            "QTime": 2,
             "params": {
                 "facet.query": [
                     'object_closure:"HP:0000924"',

diff --git a/backend/tests/fixtures/phenotype_explorer_compare.py b/backend/tests/fixtures/phenotype_explorer_compare.py
@@ -69,16 +69,16 @@ def phenotype_explorer_compare():
             "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": 1.4431977534690428,
                 "match_subsumer": None,
                 "match_subsumer_label": None,
                 "similarity": {
                     "subject_id": "HP:0004325",
                     "subject_label": None,
                     "subject_source": None,
-                    "object_id": "MP:0010771",
+                    "object_id": "MP:0002169",
                     "object_label": None,
                     "object_source": None,
                     "ancestor_id": "UPHENO:0001003",
@@ -87,10 +87,10 @@ def phenotype_explorer_compare():
                     "object_information_content": None,
                     "subject_information_content": None,
                     "ancestor_information_content": 1.4431977534690428,
-                    "jaccard_similarity": 0.3333333333333333,
+                    "jaccard_similarity": 0.16216216216216217,
                     "cosine_similarity": None,
                     "dice_similarity": None,
-                    "phenodigm_score": 0.6935891563620457,
+                    "phenodigm_score": 0.48376861011243283,
                 },
             }
         },

diff --git 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/frontend/fixtures/phenotype-explorer-compare.json b/frontend/fixtures/phenotype-explorer-compare.json
@@ -75,16 +75,16 @@
     "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": 1.4431977534690428,
       "match_subsumer": null,
       "match_subsumer_label": null,
       "similarity": {
         "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",
@@ -93,10 +93,10 @@
         "object_information_content": null,
         "subject_information_content": null,
         "ancestor_information_content": 1.4431977534690428,
-        "jaccard_similarity": 0.3333333333333333,
+        "jaccard_similarity": 0.16216216216216217,
         "cosine_similarity": null,
         "dice_similarity": null,
-        "phenodigm_score": 0.6935891563620457
+        "phenodigm_score": 0.48376861011243283
       }
     }
   },

diff --git 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