Update test flatmap: nerve cuffs, proxies, and example neuron populations

README.md

@@ -1,6 +1,13 @@
 # test-flatmap
 
-This is a simple flatmap for testing purposes. Included are features used by the `keast-5` ApiNATOMY neuron population, including spinal cord segments containing lamina VII gray matter. Because `neuronConnectivity` in the manifest specifies all of the `keast-bladder` model, parts of `keast-4`, `keast-9`, `keast-10`, and `keast-20` also appear.
+This is a simple flatmap for testing purposes. The features are included to demonstrate three key functions:
+- Example for keast-5:
+  Provides a clean example of the keast-5 ApiNATOMY neuron population—from the pelvic ganglion, through the pelvic splanchnic nerve, to spinal cord segments containing lamina VII. Other populations (e.g., keast-6) appear only because they partially share the same features.
+- Nerve cuff rendering differences:
+  Includes nerve cuffs such as the vagus nerve, the splanchnic nerve, and the external branch of the inferior laryngeal nerve. Their sizes intentionally differ based on how many neuron populations pass through them.
+  The vagus nerve is the largest example, reflecting traffic from ‘bolew-unbranched’ and the mmset4-type neuron population.
+- Proxy usage demonstration:
+  Shows how proxies work using right ovary → ovary. Here, mmset4-5 and femrep 94 target the right ovary proxy, while femrep 40 targets the general ovary.
 
 ## Map generation
 

anatomical_map.json

@@ -7,24 +7,36 @@
         "term": "UBERON:0013702",
         "name": "body proper"
     },
-    "spinal_39": {
+    "spinal_1": {
         "term": "UBERON:0016578",
         "name": "lamina VII of gray matter of spinal cord"
     },
-    "keast_5": {
-        "term": "UBERON:0018675",
-        "name": "pelvic splanchnic nerve"
+    "spinal_3": {
+        "term": "UBERON:0009624",
+        "name": "lumbar spinal nerve"
     },
-    "spinal_50": {
-        "term": "UBERON:0001780",
-        "name": "spinal nerve"
+    "spinal_4": {
+        "term": "ILX:0738371",
+        "name": "Rexed Lamina VII of T1"
     },
-    "spinal_28": {
+    "spinal_S1": {
         "term": "UBERON:0006460",
         "name": "first sacral spinal cord segment"
     },
-    "spinal_27": {
+    "spinal_L6": {
         "term": "ILX:0738432",
         "name": "Sixth lumbar spinal cord segment"
+    },
+    "respiratory_1": {
+        "term": "UBERON:0000388",
+        "name": "epiglottis"
+    },
+    "respiratory_2": {
+        "term": "UBERON:0004982",
+        "name": "mucossa of epiglottis"
+    },
+    "reproductive_1": {
+        "term": "UBERON:0002118",
+        "name": "right ovary"
     }
 }

connectivity_terms.json

@@ -0,0 +1,15 @@
+[
+    {
+        "id": [
+            "ILX:0793082",
+            []
+        ],
+        "name": "celiac ganglion- superior mesenteric ganglion complex",
+        "aliases": [
+            [
+                "UBERON:0035772",
+                []
+            ]
+        ]
+    }
+]

manifest.json

@@ -12,7 +12,9 @@
         }
     ],
     "anatomicalMap": "anatomical_map.json",
+    "connectivityTerms": "connectivity_terms.json",
     "neuronConnectivity": [
         "NPO"
-    ]
+    ],
+    "proxyFeatures": "proxy_features.json"
 }

properties.json

@@ -5,57 +5,102 @@
         }
     },
     "features": {
+        "body_1-1": {
+            "class": "body_1"
+        },
         "ganglion_1-1": {
             "models": "UBERON:0016508",
             "name": "pelvic ganglion",
             "type": "ganglion",
             "class": "auto-hide"
         },
-        "pelvic_splanchnic": {
-            "class": "keast_5",
-            "type": "nerve",
-            "models": "UBERON:0018675"
+        "ganglion_2-1": {
+            "models": "UBERON:0001989",
+            "name": "superior cervical ganglion",
+            "type": "ganglion",
+            "class": "auto-hide"
+        },
+        "ganglion_3-1": {
+            "models": "ILX:0793082",
+            "name": "Celiac Ganglion-Superior Mesenteric Ganglion Complex",
+            "type": "ganglion",
+            "class": "auto-hide"
+        },
+        "ganglion_4-1": {
+            "models": "ILX:0794910",
+            "name": "Ovarian ganglion",
+            "type": "ganglion",
+            "class": "auto-hide"
         },
-        "S50_S1": {
-            "class": "spinal_50"
+        "S1_S1": {
+            "class": "spinal_1"
         },
-        "S43_S1": {
+        "S2_S1": {
             "models": "ILX:0792853",
             "name": "Anterior root of first sacral nerve"
         },
-        "S50_L6": {
-            "class": "spinal_50"
+        "S3_S1": {
+            "models": "ILX:0790504",
+            "name": "First sacral spinal nerve"
+        },
+        "spinal_S1-1": {
+            "class": "spinal_S1"
         },
-        "S43_L6": {
+        "S1_L6": {
+            "class": "spinal_1"
+        },
+        "S2_L6": {
             "models": "ILX:0793615",
             "name": "Sixth lumbar ventral root"
         },
-        "spinal_27-1": {
-            "class": "spinal_27"
+        "S3_L6": {
+            "class": "spinal_3"
         },
-        "spinal_28-1": {
-            "class": "spinal_28"
+        "spinal_L6-1": {
+            "class": "spinal_L6"
         },
-        "S39_L6": {
-            "class": "spinal_39"
+        "spinal_4-1": {
+            "class": "spinal_4"
         },
-        "S39_S1": {
-            "class": "spinal_39"
+        "plexus_1-1": {
+            "models": "ILX:0793621",
+            "name": "external carotid nerve plexus",
+            "type": "ganglion",
+            "class": "auto-hide"
         },
-        "body_1-1": {
-            "class": "body_1"
+        "plexus_2-1": {
+            "models": "ILX:0793832",
+            "name": "Ovarian nerve plexus",
+            "type": "ganglion",
+            "class": "auto-hide"
         },
-        "ganglion_25-1": {
-            "models": "ILX:0794910",
-            "name": "Ovarian ganglion"
+        "reproductive_1-1": {
+            "class": "reproductive_1"
         },
-        "reproductive_4-1": {
-            "models": "UBERON:0000992",
-            "name": "ovary"
+        "respiratory_1-1": {
+            "class": "respiratory_1"
         },
-        "plexus_19-1": {
-            "models": "ILX:0793832",
-            "name": "Ovarian nerve plexus"
+        "respiratory_2-1": {
+            "class": "respiratory_2"
+        },
+        "nucleus_tractus_solitarius": {
+            "models": "UBERON:0009050",
+            "name": "Solitary nucleus"
+        },
+        "pelvic_splanchnic_c": {
+            "type": "nerve",
+            "models": "UBERON:0018675",
+            "name": "pelvic splanchnic nerve"
+        },
+        "nerve_1_c": {
+            "type": "nerve",
+            "models": "ILX:0738308",
+            "name": "External branch of inferior laryngeal nerve"
+        },
+        "vagus_n_c": {
+            "type": "nerve",
+            "models": "UBERON:0001759",
+            "name": "Vagus Nerve"
         }
     },
     "networks": [
@@ -89,22 +134,22 @@
                     "id": "S1_ventral_root",
                     "connects": [
                         "S1_spinal",
-                        "spinal_28-1/S1_ventral_root_end"
+                        "spinal_S1-1/S1_ventral_root_end"
                     ],
                     "contained-in": [
-                        "S43_S1",
-                        "S50_S1"
+                        "S2_S1",
+                        "S3_S1"
                     ]
                 },
                 {
                     "id": "L6_ventral_root",
                     "connects": [
                         "L6_spinal",
-                        "spinal_27-1/L6_ventral_root_end"
+                        "spinal_L6-1/L6_ventral_root_end"
                     ],
                     "contained-in": [
-                        "S43_L6",
-                        "S50_L6"
+                        "S2_L6",
+                        "S3_L6"
                     ]
                 }
             ]

proxy_features.json

@@ -0,0 +1,9 @@
+[
+    {
+        "feature": "UBERON:0000992",
+        "name": "ovary",
+        "proxies": [
+            "UBERON:0002118"
+        ]
+    }
+]