Add Triptych for set to set comparison (#591)

(making a PR from the branch because I want to play with the deploy preview) --------- Co-authored-by: Vincent Rubinetti <[email protected]>
monarch-initiative · Feb 16, 2024 · 7761950 · 7761950
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Showing 15 changed files with 263 additions and 180 deletions.
diff --git a/.DS_Store b/.DS_Store
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": 1.5540019332516637,
                 "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": 1.5540019332516637,
-                    "jaccard_similarity": 0.24,
+                    "jaccard_similarity": 0.23076923076923078,
                     "cosine_similarity": None,
                     "dice_similarity": None,
-                    "phenodigm_score": 0.61070489107293,
+                    "phenodigm_score": 0.5988454147360435,
                 },
             }
         },

diff --git a/backend/tests/fixtures/phenotype_explorer_search.py b/backend/tests/fixtures/phenotype_explorer_search.py
@@ -68,8 +68,8 @@ def phenotype_explorer_search():
                     "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)")
                 },
                 object_termset={
-                    "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"),
                     "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"),
+                    "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"),
                 },
                 subject_best_matches={
                     "ZP:0018569": BestMatch(
@@ -427,8 +427,8 @@ def phenotype_explorer_search():
                     "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"),
                 },
                 object_termset={
-                    "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"),
                     "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"),
+                    "HP:0012378": TermInfo(id="HP:0012378", label="Fatigue (HPO)"),
                 },
                 subject_best_matches={
                     "ZP:0018568": BestMatch(
@@ -622,8 +622,8 @@ def phenotype_explorer_search():
             score=7.234842285670967,
             similarity=TermSetPairwiseSimilarity(
                 subject_termset={
-                    "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"),
                     "ZP:0018568": TermInfo(id="ZP:0018568", label="primitive hemopoiesis absent, abnormal (ZPO)"),
+                    "ZP:0018569": TermInfo(id="ZP:0018569", label="myeloid cell development absent, abnormal (ZPO)"),
                 },
                 object_termset={
                     "HP:0002104": TermInfo(id="HP:0002104", label="Apnea (HPO)"),
@@ -716,16 +716,16 @@ def phenotype_explorer_search():
                     "HP:0012378": BestMatch(
                         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=None,
                         match_subsumer_label=None,
                         similarity=TermPairwiseSimilarity(
                             subject_id="HP:0012378",
                             subject_label=None,
                             subject_source=None,
-                            object_id="ZP:0018569",
+                            object_id="ZP:0018568",
                             object_label=None,
                             object_source=None,
                             ancestor_id="UPHENO:0001005",
@@ -734,10 +734,10 @@ def phenotype_explorer_search():
                             object_information_content=None,
                             subject_information_content=None,
                             ancestor_information_content=1.6836208034928104,
-                            jaccard_similarity=0.47058823529411764,
+                            jaccard_similarity=0.4444444444444444,
                             cosine_similarity=None,
                             dice_similarity=None,
-                            phenodigm_score=0.8901079388591847,
+                            phenodigm_score=0.8650294287846346,
                         ),
                     ),
                 },
@@ -881,16 +881,16 @@ def phenotype_explorer_search():
                     "HP:0002104": BestMatch(
                         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=None,
                         match_subsumer_label=None,
                         similarity=TermPairwiseSimilarity(
                             subject_id="HP:0002104",
                             subject_label=None,
                             subject_source=None,
-                            object_id="ZP:0018569",
+                            object_id="ZP:0018568",
                             object_label=None,
                             object_source=None,
                             ancestor_id="UPHENO:0034024",
@@ -899,10 +899,10 @@ def phenotype_explorer_search():
                             object_information_content=None,
                             subject_information_content=None,
                             ancestor_information_content=9.08524944639702,
-                            jaccard_similarity=0.34615384615384615,
+                            jaccard_similarity=0.3333333333333333,
                             cosine_similarity=None,
                             dice_similarity=None,
-                            phenodigm_score=1.773384910034319,
+                            phenodigm_score=1.7402346054863809,
                         ),
                     ),
                     "HP:0012378": BestMatch(

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": 3,
+            "QTime": 0,
             "params": {
                 "mm": "100%",
                 "q": "fanconi",

diff --git a/frontend/README.md b/frontend/README.md
@@ -95,22 +95,26 @@ Include the widget on your page like so:
 The widget accepts several URL parameters:
 
 - `source` - Comma-separated list of "source" phenotype IDs (set A).
-- `target` - Comma-separated list of "target" phenotype IDs (set B).
+- `target` - "target" group of phenotypes to compare to (group B).
+  See `src/api/phenotype-explorer.ts` groups for enumerated options.
 - `stylesheet` - A URI-encoded URL to a stylesheet that will be applied to the widget, for the purposes of matching its styles to your webpage.
 
 ### Events
 
 The widget also emits `message` events to the parent window when certain things change, and listens for `message` events from the parent window to receive information.
 
-#### Listens for `MessageEvent<{ source: string[], target: string[] }>`
+#### Listens for `MessageEvent<{ source: string[], target: string }>`
 
 Provide input phenotype lists to the widget when they might be [too long for a URL](https://www.google.com/search?q=max+url+length).
 
 ```js
 // get your iframe dom element somehow
 const iframe = document.querySelector("iframe");
 // send it a message
-iframe.contentWindow.postMessage({ source: ["abc"], target: ["def"] }, "*");
+iframe.contentWindow.postMessage(
+  { source: ["HP:123,HP:456"], target: "Human Diseases" },
+  "*",
+);
 ```
 
 #### Emits `MessageEvent<{ width: number; height: number; }>`

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": 1.5540019332516637,
       "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": 1.5540019332516637,
-        "jaccard_similarity": 0.24,
+        "jaccard_similarity": 0.23076923076923078,
         "cosine_similarity": null,
         "dice_similarity": null,
-        "phenodigm_score": 0.61070489107293
+        "phenodigm_score": 0.5988454147360435
       }
     }
   },