Updated organ mapping files

hubmapconsortium · Feb 22, 2024 · 17dcf72 · 17dcf72
1 parent 1c77b1a
commit 17dcf72
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Showing 3 changed files with 59 additions and 33 deletions.
diff --git a/containers/azimuth/context/organ-metadata.json b/containers/azimuth/context/organ-metadata.json
@@ -1,26 +1,32 @@
 {
+  "UBERON:0004538": "UBERON:0002113",
+  "UBERON:0004539": "UBERON:0002113",
   "UBERON:0002113": {
     "model": "kidneyref",
     "organ_level": "Kidney_L3",
     "prediction_column": "annotation.l3"
   },
-  "UBERON:0004538": "UBERON:0002113",
-  "UBERON:0004539": "UBERON:0002113",
+  "UBERON:0002168": "UBERON:0002048",
+  "UBERON:0002178": "UBERON:0002048",
+  "UBERON:0002177": "UBERON:0002048",
+  "UBERON:0002167": "UBERON:0002048",
   "UBERON:0002048": {
     "model": "lungref",
     "organ_level": "Lung_v2_finest_level",
     "prediction_column": "ann_finest_level"
   },
-  "UBERON:0001004": "UBERON:0002048",
+  "UBERON:0000947": "UBERON:0000948",
   "UBERON:0000948": {
     "model": "heartref",
     "organ_level": "Heart_L2",
-    "prediction_column": "celltype.l2"
+    "prediction_column": "celltype.l2",
+    "comment": "Aorta (UBERON:0000947) is redirected here"
   },
-  "UBERON:0000955": {
+  "UBERON:0001384": {
     "model": "humancortexref",
     "organ_level": "",
-    "prediction_column": "subclass"
+    "prediction_column": "subclass",
+    "comment": "Not redirecting brain (UBERON:0000955) to here as it is too broad"
   },
   "UBERON:0001264": {
     "model": "pancreasref",
@@ -29,7 +35,7 @@
   },
   "UBERON:0002373": {
     "model": "tonsilref",
-    "organ_level": "",
+    "organ_level": "Tonsil_v2_L2",
     "prediction_column": "celltype.l2"
   },
   "UBERON:0000178": {
@@ -44,7 +50,7 @@
   },
   "UBERON:0001013": {
     "model": "adiposeref",
-    "organ_level": "",
+    "organ_level": "Adipose_L2",
     "prediction_column": "celltype.l2"
   }
 }
diff --git a/containers/celltypist/context/organ-metadata.json b/containers/celltypist/context/organ-metadata.json
@@ -1,21 +1,37 @@
 {
+  "UBERON:0002168": "UBERON:0002048",
+  "UBERON:0002178": "UBERON:0002048",
+  "UBERON:0002177": "UBERON:0002048",
+  "UBERON:0002167": "UBERON:0002048",
   "UBERON:0002048": {
-    "model": "Human_Lung_Atlas.pkl"
+    "model": "Human_Lung_Atlas.pkl",
+    "alt_model": "Cells_Lung_Airway.pkl"
   },
-  "UBERON:0001004": "UBERON:0002048",
   "UBERON:0002097": {
     "model": "Adult_Human_Skin.pkl"
   },
-  "UBERON:0001264": {
-    "model": "Adult_Human_PancreaticIslet.pkl"
+  "UBERON:0001264": "UBERON:0000006",
+  "UBERON:0000006": {
+    "model": "Adult_Human_PancreaticIslet.pkl",
+    "comment": "Pancreas (UBERON:0001264) is redirected here"
   },
+  "UBERON:0000947": "UBERON:0000948",
   "UBERON:0000948": {
-    "model": "Healthy_Adult_Heart.pkl"
+    "model": "Healthy_Adult_Heart.pkl",
+    "comment": "Aorta (UBERON:0000947) is redirected here"
   },
   "UBERON:0002107": {
     "model": "Healthy_Human_Liver.pkl"
   },
-  "UBERON:0000955": {
-    "model": "Human_AdultAged_Hippocampus.pkl"
+  "UBERON:0002421": {
+    "model": "Human_AdultAged_Hippocampus.pkl",
+    "alt_model": "Human_Longitudinal_Hippocampus.pkl",
+    "comment": "Not redirecting brain (UBERON:0000955) to here as it is too broad"
+  },
+  "UBERON:0002108": {
+    "model": "Cells_Intestinal_Tract.pkl"
+  },
+  "UBERON:0000059": {
+    "model": "Cells_Intestinal_Tract.pkl"
   }
-}
+}
diff --git a/containers/popv/context/organ-metadata.json b/containers/popv/context/organ-metadata.json
@@ -11,19 +11,21 @@
     "model": "Bone_Marrow",
     "organ_level": "bone marrow"
   },
+  "UBERON:0004548": "UBERON:0000970",
+  "UBERON:0004549": "UBERON:0000970",
   "UBERON:0000970": {
     "model": "Eye",
     "organ_level": "eye"
   },
-  "UBERON:0004548": "UBERON:0000970",
-  "UBERON:0004549": "UBERON:0000970",
   "UBERON:0001013": {
     "model": "Fat",
     "organ_level": "adipose tissue"
   },
+  "UBERON:0000947": "UBERON:0000948",
   "UBERON:0000948": {
     "model": "Heart",
-    "organ_level": "heart"
+    "organ_level": "heart",
+    "comment": "Aorta (UBERON:0000947) is redirected here"
   },
   "UBERON:0000059": {
     "model": "Large_Intestine",
@@ -33,25 +35,23 @@
     "model": "Liver",
     "organ_level": "liver"
   },
+  "UBERON:0002168": "UBERON:0002048",
+  "UBERON:0002178": "UBERON:0002048",
+  "UBERON:0002177": "UBERON:0002048",
+  "UBERON:0002167": "UBERON:0002048",
   "UBERON:0002048": {
     "model": "Lung",
     "organ_level": "lung"
   },
-  "UBERON:0001004": {
-    "model": "Lung",
-    "organ_level": "respiratory system"
-  },
-  "UBERON:0000029": {
-    "model": "Lymph_Node",
-    "organ_level": "lymph node"
-  },
   "UBERON:0002509": {
     "model": "Lymph_Node",
-    "organ_level": "mesenteric lymph node"
+    "organ_level": "mesenteric lymph node",
+    "comment": "Generic lymph node (UBERON:0000029) is redirected here"
   },
   "UBERON:0001911": {
     "model": "Mammary",
-    "organ_level": "mammary gland"
+    "organ_level": "mammary gland",
+    "comment": "Should breast (UBERON:0000310) be redirected here?"
   },
   "UBERON:0001264": {
     "model": "Pancreas",
@@ -61,9 +61,9 @@
     "model": "Prostate",
     "organ_level": "prostate gland"
   },
-  "UBERON:0000079": {
-    "model": "Prostate",
-    "organ_level": "male reproductive system"
+  "UBERON:0001044": {
+    "model": "Salivary Gland",
+    "organ_level": ""
   },
   "UBERON:0002097": {
     "model": "Skin",
@@ -81,6 +81,10 @@
     "model": "Thymus",
     "organ_level": "thymus"
   },
+  "UBERON:0001723": {
+    "model": "Tongue",
+    "organ_level": ""
+  },
   "UBERON:0003126": {
     "model": "Trachea",
     "organ_level": "trachea"
@@ -93,4 +97,4 @@
     "model": "Vasculature",
     "organ_level": "blood vasculature"
   }
-}
+}