From fab11d0aaada66f6713fb3be7ab8d8afe4e49827 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 14:48:38 +1300 Subject: [PATCH 01/26] Update sckan version to sckan-2026-02-11. --- manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifest.json b/manifest.json index ef8a121..5298e38 100644 --- a/manifest.json +++ b/manifest.json @@ -3,7 +3,7 @@ "models": "NCBITaxon:9685", "description": "description.json", "properties": "properties.json", - "sckan-version": "sckan-2024-09-21", + "sckan-version": "sckan-2026-02-11", "sources": [ { "id": "whole-cat", From 73a811427156bdf038952b89e877b1e38df30da5 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 15:19:04 +1300 Subject: [PATCH 02/26] Add dots to render pain1 6-9 populations. --- anatomical_map.json | 20 ++++++++++++++++++++ cat_flatmap.svg | 15 +++++++++++++++ properties.json | 15 +++++++++++++++ 3 files changed, 50 insertions(+) diff --git a/anatomical_map.json b/anatomical_map.json index 4e7d3b3..8a06870 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -1371,6 +1371,10 @@ "term": "UBERON:0002141", "name": "Oculomotor nucleus" }, + "brain_56": { + "term": "UBERON:0001717", + "name": "spinal nucleus of trigeminal nerve" + }, "bolser_2": { "term": "ILX:0738309", "name": "Internal branch of inferior laryngeal nerve" @@ -1515,6 +1519,22 @@ "term": "ILX:0795060", "name": "eccrine sweat gland of the face" }, + "label_28": { + "term": "UBERON:0001456", + "name": "face" + }, + "label_29": { + "term": "UBERON:0000033", + "name": "head" + }, + "label_30": { + "term": "UBERON:0000167", + "name": "oral cavity" + }, + "label_31": { + "term": "UBERON:0002075", + "name": "viscus" + }, "vagus_n": { "term": "UBERON:0001759", "name": "Vagus Nerve" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index bea4768..6e6bbcf 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20075,6 +20075,9 @@ .id(brain_55-1) + + .id(brain_56-1) + Labels @@ -20733,6 +20736,18 @@ .id(label_27-1) + + .id(label_31-1) + + + .id(label_30-1) + + + .id(label_29-1) + + + .id(label_28-1) + Ganglia diff --git a/properties.json b/properties.json index 2e37c9f..9355e5c 100644 --- a/properties.json +++ b/properties.json @@ -2223,6 +2223,9 @@ "brain_55-1": { "class": "brain_55" }, + "brain_56-1": { + "class": "brain_56" + }, "brain_8-1": { "class": "brain_8" }, @@ -3644,6 +3647,18 @@ "label_27-1": { "class": "label_27" }, + "label_28-1": { + "class": "label_28" + }, + "label_29-1": { + "class": "label_29" + }, + "label_30-1": { + "class": "label_30" + }, + "label_31-1": { + "class": "label_31" + }, "CNVII_c": { "type": "nerve", "models": "UBERON:0001647" From d6de9c1f8cfde23dd983b3ab0681a170b4fd7ff5 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 15:30:33 +1300 Subject: [PATCH 03/26] Add a dot and aliases to render gastin 6-8. --- anatomical_map.json | 4 ++++ cat_flatmap.svg | 6 ++++++ connectivity_terms.json | 21 +++++++++++++++++++++ properties.json | 9 +++++++++ 4 files changed, 40 insertions(+) diff --git a/anatomical_map.json b/anatomical_map.json index 8a06870..f14878f 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -687,6 +687,10 @@ "term": "UBERON:0002017", "name": "portal vein" }, + "digestive_93": { + "term": "ILX:0795342", + "name": "upper part of the anal canal" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 6e6bbcf..7f75a6c 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -10631,6 +10631,9 @@ + + .id(digestive_93-1) + .id(digestive_79-1) @@ -20895,6 +20898,9 @@ .id(ganglion_27-1) + + .id(ganglion_28-1) + Plexus diff --git a/connectivity_terms.json b/connectivity_terms.json index 874cfcc..6a2199e 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1873,5 +1873,26 @@ [] ] ] + }, + { + "id": [ + "UBERON:0001155", + [] + ], + "name": "colon", + "aliases": [ + [ + "UBERON:0001158", + [] + ], + [ + "UBERON:0001159", + [] + ], + [ + "ILX:0773031", + [] + ] + ] } ] \ No newline at end of file diff --git a/properties.json b/properties.json index 9355e5c..75fc155 100644 --- a/properties.json +++ b/properties.json @@ -2059,6 +2059,12 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_28-1": { + "models": "ILX:0795345", + "name": "myenteric nerve plexus ganglion of large intestine", + "type": "ganglion", + "class": "auto-hide" + }, "body_6-1": { "class": "body_6" }, @@ -2574,6 +2580,9 @@ "digestive_92-1": { "class": "digestive_92" }, + "digestive_93-1": { + "class": "digestive_93" + }, "digestive_9-1": { "class": "digestive_9" }, From 00bedc30df63d721010bde12c74031377a9aa0bb Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 15:41:48 +1300 Subject: [PATCH 04/26] Add a dot and aliases to render gastint 9, 10. --- cat_flatmap.svg | 3 +++ connectivity_terms.json | 8 ++++++++ properties.json | 6 ++++++ 3 files changed, 17 insertions(+) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 7f75a6c..80efc79 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20901,6 +20901,9 @@ .id(ganglion_28-1) + + .id(ganglion_29-1) + Plexus diff --git a/connectivity_terms.json b/connectivity_terms.json index 6a2199e..0a4b029 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1881,6 +1881,14 @@ ], "name": "colon", "aliases": [ + [ + "UBERON:0001156", + [] + ], + [ + "UBERON:0001157", + [] + ], [ "UBERON:0001158", [] diff --git a/properties.json b/properties.json index 75fc155..569aa82 100644 --- a/properties.json +++ b/properties.json @@ -2065,6 +2065,12 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_29-1": { + "models": "UBERON:0001809", + "name": "enteric ganglion", + "type": "ganglion", + "class": "auto-hide" + }, "body_6-1": { "class": "body_6" }, From c7751c22f9c6e8571793a83345b2d5fc7972d230 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 15:53:03 +1300 Subject: [PATCH 05/26] Add dots to render pain1 1-5, 10, and 12. --- anatomical_map.json | 20 ++++++++++++++++++++ cat_flatmap.svg | 15 +++++++++++++++ properties.json | 12 ++++++++++++ 3 files changed, 47 insertions(+) diff --git a/anatomical_map.json b/anatomical_map.json index f14878f..5a66012 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -1379,6 +1379,10 @@ "term": "UBERON:0001717", "name": "spinal nucleus of trigeminal nerve" }, + "brain_57": { + "term": "UBERON:0002945", + "name": "ventral posteromedial nucleus of thalamus" + }, "bolser_2": { "term": "ILX:0738309", "name": "Internal branch of inferior laryngeal nerve" @@ -1539,6 +1543,22 @@ "term": "UBERON:0002075", "name": "viscus" }, + "label_32": { + "term": "UBERON:0001484", + "name": "articular capsule" + }, + "label_33": { + "term": "UBERON:0002097", + "name": "skin of body" + }, + "label_34": { + "term": "UBERON:0001015", + "name": "musculature" + }, + "label_35": { + "term": "UBERON:0001630", + "name": "muscle organ" + }, "vagus_n": { "term": "UBERON:0001759", "name": "Vagus Nerve" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 80efc79..f9e3a21 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20081,6 +20081,9 @@ .id(brain_56-1) + + .id(brain_57-1) + Labels @@ -20751,6 +20754,18 @@ .id(label_28-1) + + .id(label_32-1) + + + .id(label_33-1) + + + .id(label_34-1) + + + .id(label_35-1) + Ganglia diff --git a/properties.json b/properties.json index 569aa82..a52fe29 100644 --- a/properties.json +++ b/properties.json @@ -3674,6 +3674,18 @@ "label_31-1": { "class": "label_31" }, + "label_32-1": { + "class": "label_32" + }, + "label_33-1": { + "class": "label_33" + }, + "label_34-1": { + "class": "label_34" + }, + "label_35-1": { + "class": "label_35" + }, "CNVII_c": { "type": "nerve", "models": "UBERON:0001647" From b9c456ef57e728b6e793cabda0478b07357d16c6 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:02:46 +1300 Subject: [PATCH 06/26] Add dots to render gastint 3, 4, and 17. --- anatomical_map.json | 24 ++++++++++++++++++++++++ cat_flatmap.svg | 24 ++++++++++++++++++++++++ connectivity_terms.json | 12 ------------ properties.json | 34 ++++++++++++++++++++++++++++++++-- 4 files changed, 80 insertions(+), 14 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index 5a66012..0e10d24 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -691,6 +691,30 @@ "term": "ILX:0795342", "name": "upper part of the anal canal" }, + "digestive_94": { + "term": "UBERON:0001902", + "name": "epithelium of small intestine" + }, + "digestive_95": { + "term": "ILX:0771006", + "name": "wall of duodenum" + }, + "digestive_96": { + "term": "UBERON:0014390", + "name": "muscle layer of ileum" + }, + "digestive_97": { + "term": "UBERON:0012377", + "name": "muscle layer of jejunum" + }, + "digestive_98": { + "term": "ILX:0773238", + "name": "Muscle layer of transverse colon" + }, + "digestive_99": { + "term": "ILX:0795341", + "name": "muscle layer of proximal colon" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index f9e3a21..1b262e4 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20766,6 +20766,24 @@ .id(label_35-1) + + .id(digestive_94-1) + + + .id(digestive_96-1) + + + .id(digestive_97-1) + + + .id(digestive_98-1) + + + .id(digestive_99-1) + + + .id(digestive_95-1) + Ganglia @@ -20919,6 +20937,12 @@ .id(ganglion_29-1) + + .id(ganglion_30-1) + + + .id(ganglion_31-1) + Plexus diff --git a/connectivity_terms.json b/connectivity_terms.json index 0a4b029..e907c28 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -491,18 +491,6 @@ ] ] }, - { - "id": [ - "UBERON:0002115", - [] - ], - "aliases": [ - [ - "ILX:0793735", - [] - ] - ] - }, { "id": [ "UBERON:0000988", diff --git a/properties.json b/properties.json index a52fe29..5fe7ce0 100644 --- a/properties.json +++ b/properties.json @@ -2071,6 +2071,18 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_30-1": { + "models": "ILX:0795348", + "name": "submucosal nerve plexus ganglion of small intestine", + "type": "ganglion", + "class": "auto-hide" + }, + "ganglion_31-1": { + "models": "ILX:0793735", + "name": "Myenteric ganglion of small intestine", + "type": "ganglion", + "class": "auto-hide" + }, "body_6-1": { "class": "body_6" }, @@ -2577,6 +2589,9 @@ "digestive_89-1": { "class": "digestive_89" }, + "digestive_9-1": { + "class": "digestive_9" + }, "digestive_90-1": { "class": "digestive_90" }, @@ -2589,8 +2604,23 @@ "digestive_93-1": { "class": "digestive_93" }, - "digestive_9-1": { - "class": "digestive_9" + "digestive_94-1": { + "class": "digestive_94" + }, + "digestive_95-1": { + "class": "digestive_95" + }, + "digestive_96-1": { + "class": "digestive_96" + }, + "digestive_97-1": { + "class": "digestive_97" + }, + "digestive_98-1": { + "class": "digestive_98" + }, + "digestive_99-1": { + "class": "digestive_99" }, "endocrine_1-1": { "class": "endocrine_1" From 4ffc13252041057a080ce65080fb4baadb2ce625 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:07:44 +1300 Subject: [PATCH 07/26] Add aliases and a dot to render portal 2-5. --- anatomical_map.json | 4 ++-- connectivity_terms.json | 43 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 45 insertions(+), 2 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index 0e10d24..4d0c28c 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -172,8 +172,8 @@ "name": "cardiac muscle of left ventricle" }, "cardio_24": { - "term": "UBERON:0001986", - "name": "endothelium" + "term": "UBERON:0015129", + "name": "Epicardial Fat" }, "cardio_25": { "term": "UBERON:0003381", diff --git a/connectivity_terms.json b/connectivity_terms.json index e907c28..a951fc4 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1890,5 +1890,48 @@ [] ] ] + }, + { + "id": [ + "ILX:0793558", + [] + ], + "name": "Distal stomach", + "aliases": [ + [ + "UBERON:0001165", + [] + ] + ] + }, + { + "id": [ + "ILX:0793658", + [] + ], + "name": "Proximal stomach", + "aliases": [ + [ + "UBERON:0005477", + [] + ], + [ + "UBERON:0001161", + [] + ] + ] + }, + { + "id": [ + "ILX:0793656", + [] + ], + "name": "myenteric nerve plexus of stomach", + "aliases": [ + [ + "ILX:0795344", + [] + ] + ] } ] \ No newline at end of file From 38a035b1d3c41e6f1888cfa223eca5f8c9154d9c Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:08:43 +1300 Subject: [PATCH 08/26] Add ventrolateral periaqueductal gray. --- anatomical_map.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/anatomical_map.json b/anatomical_map.json index 4d0c28c..7ea585b 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -1244,7 +1244,7 @@ "name": "Barrington's nucleus" }, "brain_14": { - "term": "UBERON:0003040", + "term": "ILX:0793626", "name": "Ventrolateral Periaqueductal Gray" }, "brain_15": { From 3605ede29074458b120594b7fff6cf3147e09e29 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:09:48 +1300 Subject: [PATCH 09/26] Add aliases to CG-SMGC. --- connectivity_terms.json | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/connectivity_terms.json b/connectivity_terms.json index a951fc4..816b53b 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -245,6 +245,22 @@ [ "UBERON:0011926", [] + ], + [ + "ILX:0795513", + [] + ], + [ + "ILX:0795514", + [] + ], + [ + "ILX:0795515", + [] + ], + [ + "ILX:0795516", + [] ] ] }, From 773b52938acb692ca1867b4a1b566036cc2d99fa Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:22:56 +1300 Subject: [PATCH 10/26] Add a dot and an alias to render liver 131 and 132. --- anatomical_map.json | 4 ++++ cat_flatmap.svg | 5 ++++- connectivity_terms.json | 2 +- properties.json | 3 +++ 4 files changed, 12 insertions(+), 2 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index 7ea585b..9303cf3 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -715,6 +715,10 @@ "term": "ILX:0795341", "name": "muscle layer of proximal colon" }, + "digestive_100": { + "term": "UBERON:0005436", + "name": "common hepatic artery" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 1b262e4..8377bfa 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20781,7 +20781,10 @@ .id(digestive_99-1) - + + .id(digestive_100-1) + + .id(digestive_95-1) diff --git a/connectivity_terms.json b/connectivity_terms.json index 816b53b..b444b03 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1616,7 +1616,7 @@ [] ], [ - "CL:0009094", + "UBERON:0001639", [] ] ] diff --git a/properties.json b/properties.json index 5fe7ce0..0c111da 100644 --- a/properties.json +++ b/properties.json @@ -2622,6 +2622,9 @@ "digestive_99-1": { "class": "digestive_99" }, + "digestive_100-1": { + "class": "digestive_100" + }, "endocrine_1-1": { "class": "endocrine_1" }, From bd11e5aa58ba56ef68dad831e5bc3c75c50f22ec Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:34:45 +1300 Subject: [PATCH 11/26] Add dots to render gastint 12, 14, and 18. --- anatomical_map.json | 12 ++++++++++++ cat_flatmap.svg | 20 +++++++++++++++++--- properties.json | 15 +++++++++++++++ 3 files changed, 44 insertions(+), 3 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index 9303cf3..06c47bf 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -719,6 +719,18 @@ "term": "UBERON:0005436", "name": "common hepatic artery" }, + "digestive_101": { + "term": "UBERON:0011198", + "name": "muscle layer of large intestine" + }, + "digestive_102": { + "term": "UBERON:0001278", + "name": "epithelium of large intestine" + }, + "digestive_103": { + "term": "UBERON:0004222", + "name": "stomach smooth muscle" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 8377bfa..4677592 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -11130,6 +11130,20 @@ + + + .id(digestive_101-1) + + + .id(ganglion_28-1) + + + .id(ganglion_32-1) + + + .id(digestive_102-1) + + .id(endocrine_2-1) @@ -20787,6 +20801,9 @@ .id(digestive_95-1) + + .id(digestive_103-1) + Ganglia @@ -20934,9 +20951,6 @@ .id(ganglion_27-1) - - .id(ganglion_28-1) - .id(ganglion_29-1) diff --git a/properties.json b/properties.json index 0c111da..c7a1541 100644 --- a/properties.json +++ b/properties.json @@ -2083,6 +2083,12 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_32-1": { + "models": "ILX:0795349", + "name": "submucosal nerve plexus ganglion of large intestine", + "type": "ganglion", + "class": "auto-hide" + }, "body_6-1": { "class": "body_6" }, @@ -2625,6 +2631,15 @@ "digestive_100-1": { "class": "digestive_100" }, + "digestive_101-1": { + "class": "digestive_101" + }, + "digestive_102-1": { + "class": "digestive_102" + }, + "digestive_103-1": { + "class": "digestive_103" + }, "endocrine_1-1": { "class": "endocrine_1" }, From 1e7a18ce246a5a137d967f24d26749be62a8d9c3 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 26 Feb 2026 17:43:08 +1300 Subject: [PATCH 12/26] Add dots and an alias to render pain1/11. --- anatomical_map.json | 12 ++++++++++++ cat_flatmap.svg | 9 +++++++++ properties.json | 12 ++++++++++++ proxy_features.json | 7 +++++++ 4 files changed, 40 insertions(+) diff --git a/anatomical_map.json b/anatomical_map.json index 06c47bf..d704f0d 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -1423,6 +1423,18 @@ "term": "UBERON:0002945", "name": "ventral posteromedial nucleus of thalamus" }, + "brain_58": { + "term": "UBERON:0002866", + "name": "caudal part of spinal trigeminal nucleus" + }, + "brain_59": { + "term": "UBERON:0002873", + "name": "interpolar part of spinal trigeminal nucleus" + }, + "brain_60": { + "term": "UBERON:0002591", + "name": "oral part of spinal trigeminal nucleus" + }, "bolser_2": { "term": "ILX:0738309", "name": "Internal branch of inferior laryngeal nerve" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 4677592..afc7826 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20098,6 +20098,15 @@ .id(brain_57-1) + + .id(brain_58-1) + + + .id(brain_59-1) + + + .id(brain_50-1) + Labels diff --git a/properties.json b/properties.json index c7a1541..eed0288 100644 --- a/properties.json +++ b/properties.json @@ -2256,6 +2256,18 @@ "brain_56-1": { "class": "brain_56" }, + "brain_57-1": { + "class": "brain_57" + }, + "brain_58-1": { + "class": "brain_58" + }, + "brain_59-1": { + "class": "brain_59" + }, + "brain_60-1": { + "class": "brain_60" + }, "brain_8-1": { "class": "brain_8" }, diff --git a/proxy_features.json b/proxy_features.json index bd0ca10..b6095ec 100644 --- a/proxy_features.json +++ b/proxy_features.json @@ -12,5 +12,12 @@ "proxies": [ "UBERON:0002844" ] + }, + { + "feature": "UBERON:0004170", + "name": "Spinal cord ventral commissure", + "proxies": [ + "UBERON:0006469" + ] } ] From c8b29dc4c6167c087cca67d7b7b0803966aecede Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 09:50:17 +1300 Subject: [PATCH 13/26] Fix the annotation of dorsal root of spinal cords. --- cat_flatmap.svg | 102 +++++++++++++--------------------------- connectivity_terms.json | 17 +++++++ properties.json | 101 +++++++++++++++++---------------------- proxy_features.json | 7 +++ 4 files changed, 99 insertions(+), 128 deletions(-) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index afc7826..81ed744 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -910,75 +910,39 @@ .id(S44_T5) - - .id(S44_T6-1) - - .id(S44_T6) - - - - .id(S44_T7-1) - - .id(S44_T7) - - - - .id(S44_T8-1) - - .id(S44_T8) - - - - .id(S44_T9-1) - - .id(S44_T9) - - - - .id(S44_T10-1) - - .id(S44_T10) - - - - .id(S44_T11-1) - - .id(S44_T11) - - - - .id(S44_T12-1) - - .id(S44_T12) - - - - .id(S44_T13_L) - - .id(S44_T13_R) - - .id(S44_T13) - - - - - .id(S44_L1-1) - - .id(S44_L1) - - - - .id(S44_L2-1) - - .id(S44_L2) - - - - .id(S44_L3-1) - - .id(S44_L3) - - + + .id(S44_T6) + + + .id(S44_T7) + + + .id(S44_T8) + + + .id(S44_T9) + + + .id(S44_T10) + + + .id(S44_T11) + + + .id(S44_T12) + + + .id(S44_T13) + + + .id(S44_L1) + + + .id(S44_L2) + + + .id(S44_L3) + .id(S44_L4) diff --git a/connectivity_terms.json b/connectivity_terms.json index b444b03..3ef552a 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1949,5 +1949,22 @@ [] ] ] + }, + { + "id": [ + "ILX:0795492", + [] + ], + "name": "posterior root of thirteenth thoracic nerve", + "aliases": [ + [ + "ILX:0795050", + [] + ], + [ + "ILX:0795049", + [] + ] + ] } ] \ No newline at end of file diff --git a/properties.json b/properties.json index eed0288..f0a593b 100644 --- a/properties.json +++ b/properties.json @@ -1252,145 +1252,128 @@ "name": "Anterior root of fourth sacral nerve" }, "S44_C1": { - "class": "spinal_44" + "models": "ILX:0784521", + "name": "Posterior root of first cervical nerve" }, "S44_C2": { - "class": "spinal_44" + "models": "ILX:0785587", + "name": "Posterior root of second cervical nerve" }, "S44_C3": { - "class": "spinal_44" + "models": "ILX:0784978", + "name": "Posterior root of third cervical nerve" }, "S44_C4": { - "class": "spinal_44" + "models": "ILX:0788437", + "name": "Posterior root of fourth cervical nerve" }, "S44_C5": { - "class": "spinal_44" + "models": "ILX:0785440", + "name": "Posterior root of fifth cervical nerve" }, "S44_C6": { - "class": "spinal_44" + "models": "ILX:0792748", + "name": "Posterior root of sixth cervical nerve" }, "S44_C7": { - "class": "spinal_44" + "models": "ILX:0789105", + "name": "Posterior root of seventh cervical nerve" }, "S44_C8": { - "class": "spinal_44" + "models": "ILX:0787870", + "name": "Posterior root of eighth cervical nerve" }, "S44_L1": { - "class": "spinal_44" - }, - "S44_L1-1": { "models": "ILX:0787779", "name": "posterior root of first lumbar nerve" }, "S44_L2": { - "class": "spinal_44" - }, - "S44_L2-1": { "models": "ILX:0792058", "name": "posterior root of second lumbar nerve" }, "S44_L3": { - "class": "spinal_44" - }, - "S44_L3-1": { "models": "ILX:0787227", "name": "posterior root of third lumbar nerve" }, "S44_L4": { - "class": "spinal_44" + "models": "ILX:0786747", + "name": "posterior root of fourth lumbar nerve" }, "S44_L5": { - "class": "spinal_44" + "models": "ILX:0785201", + "name": "posterior root of fifth lumbar nerve" }, "S44_L6": { - "class": "spinal_44" + "models": "ILX:0795491", + "name": "posterior root of sixth lumbar nerve" }, "S44_T1": { - "class": "spinal_44" + "models": "ILX:0785632", + "name": "posterior root of first thoracic nerve" }, "S44_T2": { - "class": "spinal_44" + "models": "ILX:0791802", + "name": "posterior root of second thoracic nerve" }, "S44_T3": { - "class": "spinal_44" + "models": "ILX:0789246", + "name": "posterior root of third thoracic nerve" }, "S44_T4": { - "class": "spinal_44" + "models": "ILX:0785816", + "name": "posterior root of fourth thoracic nerve" }, "S44_T5": { - "class": "spinal_44" + "models": "ILX:0788907", + "name": "posterior root of fifth thoracic nerve" }, "S44_T6": { - "class": "spinal_44" - }, - "S44_T6-1": { "models": "ILX:0785909", "name": "posterior root of sixth thoracic nerve" }, "S44_T7": { - "class": "spinal_44" - }, - "S44_T7-1": { "models": "ILX:0784605", "name": "posterior root of seventh thoracic nerve" }, "S44_T8": { - "class": "spinal_44" - }, - "S44_T8-1": { "models": "ILX:0792624", "name": "posterior root of eighth thoracic nerve" }, "S44_T9": { - "class": "spinal_44" - }, - "S44_T9-1": { "models": "ILX:0789741", "name": "posterior root of ninth thoracic nerve" }, "S44_T10": { - "class": "spinal_44" - }, - "S44_T10-1": { "models": "ILX:0789892", "name": "posterior root of tenth thoracic nerve" }, "S44_T11": { - "class": "spinal_44" - }, - "S44_T11-1": { "models": "ILX:0790338", "name": "posterior root of eleventh thoracic nerve" }, "S44_T12": { - "class": "spinal_44" - }, - "S44_T12-1": { "models": "ILX:0787665", "name": "posterior root of twelfth thoracic nerve" }, "S44_T13": { - "class": "spinal_44" - }, - "S44_T13_L": { - "models": "ILX:0795050", - "name": "Posterior root of left thirteenth thoracic nerve" - }, - "S44_T13_R": { - "models": "ILX:0795049", - "name": "Posterior root of right thirteenth thoracic nerve" + "models": "ILX:0795492", + "name": "posterior root of thirteenth thoracic nerve" }, "S44_S1": { - "class": "spinal_44" + "models": "ILX:0789717", + "name": "Posterior root of right first sacral nerve" }, "S44_S2": { - "class": "spinal_44" + "models": "ILX:0790532", + "name": "Posterior root of second sacral nerve" }, "S44_S3": { - "class": "spinal_44" + "models": "ILX:0785877", + "name": "Posterior root of third sacral nerve" }, "S44_S4": { - "class": "spinal_44" + "models": "ILX:0787750", + "name": "Posterior root of fourth sacral nerve" }, "S45_C1": { "models": "UBERON:0002838", diff --git a/proxy_features.json b/proxy_features.json index b6095ec..3f279a6 100644 --- a/proxy_features.json +++ b/proxy_features.json @@ -19,5 +19,12 @@ "proxies": [ "UBERON:0006469" ] + }, + { + "feature": "UBERON:0002261", + "name": "dorsal root of spinal cord", + "proxies": [ + "ILX:0786747" + ] } ] From 1db33d3e25a93f6b5f20eea8ed5bf239a45eb884 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 09:55:45 +1300 Subject: [PATCH 14/26] Fix aliases and properties arounf the spines. --- cat_flatmap.svg | 62 +++---- connectivity_terms.json | 396 ++++++++++++++++++++++++++++++++++++---- properties.json | 10 +- 3 files changed, 400 insertions(+), 68 deletions(-) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 81ed744..5a63bcb 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -1377,7 +1377,7 @@ .id(S33_S4) - .closed interior id(spinal_32-31) + .id(spinal_32-31) @@ -1427,7 +1427,7 @@ .id(S33_S3) - .closed interior id(spinal_32-30) + .id(spinal_32-30) @@ -1477,7 +1477,7 @@ .id(S33_S2) - .closed interior id(spinal_32-29) + .id(spinal_32-29) @@ -1533,7 +1533,7 @@ .id(S33_S1) - .closed interior id(spinal_32-28) + .id(spinal_32-28) @@ -1598,7 +1598,7 @@ .id(S33_L6) - .closed interior id(spinal_32-27) + .id(spinal_32-27) @@ -1660,7 +1660,7 @@ .id(S33_L5) - .closed interior id(spinal_32-26) + .id(spinal_32-26) @@ -1722,7 +1722,7 @@ .id(S33_L4) - .closed interior id(spinal_32-25) + .id(spinal_32-25) @@ -1778,7 +1778,7 @@ .id(S33_L3) - .closed interior id(spinal_32-24) + .id(spinal_32-24) @@ -1834,7 +1834,7 @@ .id(S33_L2) - .closed interior id(spinal_32-23) + .id(spinal_32-23) @@ -1893,7 +1893,7 @@ .id(S33_L1) - .closed interior id(spinal_32-22) + .id(spinal_32-22) @@ -1946,7 +1946,7 @@ .id(S33_T13) - .closed interior id(spinal_32-21) + .id(spinal_32-21) @@ -2002,7 +2002,7 @@ .id(S33_T12) - .closed interior id(spinal_32-20) + .id(spinal_32-20) @@ -2058,7 +2058,7 @@ .id(S33_T11) - .closed interior id(spinal_32-19) + .id(spinal_32-19) @@ -2111,7 +2111,7 @@ .id(S33_T10) - .closed interior id(spinal_32-18) + .id(spinal_32-18) @@ -2164,7 +2164,7 @@ .id(S33_T9) - .closed interior id(spinal_32-17) + .id(spinal_32-17) @@ -2214,7 +2214,7 @@ .id(S33_T8) - .closed interior id(spinal_32-16) + .id(spinal_32-16) @@ -2267,7 +2267,7 @@ .id(S33_T7) - .closed interior id(spinal_32-15) + .id(spinal_32-15) @@ -2317,7 +2317,7 @@ .id(S33_T6) - .closed interior id(spinal_32-14) + .id(spinal_32-14) @@ -2367,7 +2367,7 @@ .id(S33_T5) - .closed interior id(spinal_32-13) + .id(spinal_32-13) @@ -2417,7 +2417,7 @@ .id(S33_T4) - .closed interior id(spinal_32-12) + .id(spinal_32-12) @@ -2467,7 +2467,7 @@ .id(S33_T3) - .closed interior id(spinal_32-11) + .id(spinal_32-11) @@ -2520,7 +2520,7 @@ .id(S33_T2) - .closed interior id(spinal_32-10) + .id(spinal_32-10) @@ -2579,7 +2579,7 @@ .id(S33_T1) - .closed interior id(spinal_32-9) + .id(spinal_32-9) @@ -2644,7 +2644,7 @@ .id(S33_C8) - .closed interior id(spinal_32-8) + .id(spinal_32-8) @@ -2712,7 +2712,7 @@ .id(S33_C7) - .closed interior id(spinal_32-7) + .id(spinal_32-7) @@ -2774,7 +2774,7 @@ .id(S33_C6) - .closed interior id(spinal_32-6) + .id(spinal_32-6) @@ -2839,7 +2839,7 @@ .id(S33_C5) - .closed interior id(spinal_32-5) + .id(spinal_32-5) @@ -2901,7 +2901,7 @@ .id(S33_C4) - .closed interior id(spinal_32-4) + .id(spinal_32-4) @@ -2957,7 +2957,7 @@ .id(S33_C3) - .closed interior id(spinal_32-3) + .id(spinal_32-3) @@ -3010,7 +3010,7 @@ .id(S33_C2) - .closed interior id(spinal_32-2) + .id(spinal_32-2) @@ -3060,7 +3060,7 @@ .id(S33_C1) - .closed interior id(spinal_32-1) + .id(spinal_32-1) diff --git a/connectivity_terms.json b/connectivity_terms.json index 3ef552a..3ea9837 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1706,38 +1706,6 @@ "ILX:0795030", [] ], - [ - "ILX:0795036", - [] - ], - [ - "ILX:0795033", - [] - ], - [ - "ILX:0795037", - [] - ], - [ - "ILX:0795035", - [] - ], - [ - "ILX:0795032", - [] - ], - [ - "ILX:0795038", - [] - ], - [ - "ILX:0795039", - [] - ], - [ - "ILX:0795034", - [] - ], [ "ILX:0795045", [] @@ -1966,5 +1934,369 @@ [] ] ] + }, + { + "id": [ + "UBERON:0018680", + [] + ], + "name": "greater splanchnic nerve", + "aliases": [ + [ + "ILX:0796950", + [] + ] + ] + }, + { + "id": [ + "UBERON:0018681", + [] + ], + "name": "lesser splanchnic nerve", + "aliases": [ + [ + "ILX:0796952", + [] + ] + ] + }, + { + "id": [ + "ILX:0785632", + [] + ], + "name": "Posterior root of first thoracic nerve", + "aliases": [ + [ + "ILX:0790352", + [] + ] + ] + }, + { + "id": [ + "ILX:0791802", + [] + ], + "name": "Posterior root of second thoracic nerve", + "aliases": [ + [ + "ILX:0784952", + [] + ] + ] + }, + { + "id": [ + "ILX:0789246", + [] + ], + "name": "Posterior root of third thoracic nerve", + "aliases": [ + [ + "ILX:0788815", + [] + ] + ] + }, + { + "id": [ + "ILX:0784605", + [] + ], + "name": "Posterior root of seventh thoracic nerve", + "aliases": [ + [ + "ILX:0788023", + [] + ] + ] + }, + { + "id": [ + "ILX:0787870", + [] + ], + "name": "Posterior root of eight cervical nerve", + "aliases": [ + [ + "ILX:0792093", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006470" + ] + ], + "name": "gray matter of spinal cord/eight cervical spinal cord segment", + "aliases": [ + [ + "ILX:0797431", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006457" + ] + ], + "name": "gray matter of spinal cord/first thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0797432", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006458" + ] + ], + "name": "gray matter of spinal cord/second thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0797433", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006459" + ] + ], + "name": "gray matter of spinal cord/third thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0797434", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006455" + ] + ], + "name": "gray matter of spinal cord/seventh thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0796498", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006456" + ] + ], + "name": "gray matter of spinal cord/eight thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795032", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006465" + ] + ], + "name": "gray matter of spinal cord/ninth thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795033", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006466" + ] + ], + "name": "gray matter of spinal cord/tenth thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795034", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006467" + ] + ], + "name": "gray matter of spinal cord/eleventh thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795035", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006468" + ] + ], + "name": "gray matter of spinal cord/twelfth thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795036", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "ILX:0793357" + ] + ], + "name": "gray matter of spinal cord/thirteenth thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795037", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006448" + ] + ], + "name": "gray matter of spinal cord/first lumbar spinal cord segment", + "aliases": [ + [ + "ILX:0795038", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006450" + ] + ], + "name": "gray matter of spinal cord/second lumbar spinal cord segment", + "aliases": [ + [ + "ILX:0795039", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002844", + [] + ], + "name": "eight cervical dorsal root ganglion", + "aliases": [ + [ + "ILX:0785251", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002845", + [] + ], + "name": "first thoracic dorsal root ganglion", + "aliases": [ + [ + "ILX:0784660", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002846", + [] + ], + "name": "second thoracic dorsal root ganglion", + "aliases": [ + [ + "ILX:0785420", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002847", + [] + ], + "name": "third thoracic dorsal root ganglion", + "aliases": [ + [ + "ILX:0791100", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002850", + [] + ], + "name": "seventh thoracic dorsal root ganglion", + "aliases": [ + [ + "ILX:0785878", + [] + ] + ] + }, + { + "id": [ + "ILX:0793359", + [] + ], + "name": "thirteenth thoracic dorsal root ganglion", + "aliases": [ + [ + "ILX:0795494", + [] + ] + ] } ] \ No newline at end of file diff --git a/properties.json b/properties.json index f0a593b..2c0065f 100644 --- a/properties.json +++ b/properties.json @@ -1360,19 +1360,19 @@ "name": "posterior root of thirteenth thoracic nerve" }, "S44_S1": { - "models": "ILX:0789717", - "name": "Posterior root of right first sacral nerve" + "models": "ILX:0791633", + "name": "Posterior root of first sacral nerve" }, "S44_S2": { - "models": "ILX:0790532", + "models": "ILX:0788723", "name": "Posterior root of second sacral nerve" }, "S44_S3": { - "models": "ILX:0785877", + "models": "ILX:0786145", "name": "Posterior root of third sacral nerve" }, "S44_S4": { - "models": "ILX:0787750", + "models": "ILX:0785338", "name": "Posterior root of fourth sacral nerve" }, "S45_C1": { From cef07e860959b9b2fa082302e38e9d2ac97877f7 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 10:53:03 +1300 Subject: [PATCH 15/26] Add dots and aliases to render gastint populations. --- anatomical_map.json | 32 ++++++++++++++++++++ cat_flatmap.svg | 54 ++++++++++++++++++++++++++++++++-- properties.json | 72 +++++++++++++++++++++++++++++++++++++++++++++ proxy_features.json | 7 +++++ 4 files changed, 163 insertions(+), 2 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index d704f0d..320561c 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -731,6 +731,38 @@ "term": "UBERON:0004222", "name": "stomach smooth muscle" }, + "digestive_104": { + "term": "UBERON:8410061", + "name": "Longitudinal Muscle Layer of Colon" + }, + "digestive_105": { + "term": "UBERON:0012419", + "name": "Taenia coli" + }, + "digestive_106": { + "term": "UBERON:0003832", + "name": "esophagus muscle" + }, + "digestive_107": { + "term": "UBERON:0004239", + "name": "small intestine smooth muscle" + }, + "digestive_108": { + "term": "UBERON:0018111", + "name": "muscle layer of rectum" + }, + "digestive_109": { + "term": "UBERON:0003354", + "name": "anal canal epithelium" + }, + "digestive_110": { + "term": "UBERON:0012490", + "name": "muscle layer of anal canal" + }, + "digestive_111": { + "term": "UBERON:0015716", + "name": "epithelium of rectum" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 5a63bcb..4b737cf 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -10595,7 +10595,7 @@ - + .id(digestive_93-1) @@ -11108,6 +11108,17 @@ .id(digestive_102-1) + + + .id(digestive_104-1) + + + .id(ganglion_33-1) + + + .id(digestive_105-1) + + .id(endocrine_2-1) @@ -20777,6 +20788,24 @@ .id(digestive_103-1) + + .id(digestive_106-1) + + + .id(digestive_107-1) + + + .id(digestive_108-1) + + + .id(digestive_109-1) + + + .id(digestive_110-1) + + + .id(digestive_111-1) + Ganglia @@ -20930,9 +20959,18 @@ .id(ganglion_30-1) - + .id(ganglion_31-1) + + .id(ganglion_34-1) + + + .id(ganglion_35-1) + + + .id(ganglion_36-1) + Plexus @@ -20991,6 +21029,18 @@ .id(plexus_20-1) + + .id(plexus_21-1) + + + .id(plexus_22-1) + + + .id(plexus_23-1) + + + .id(plexus_24-1) + Nodes diff --git a/properties.json b/properties.json index 2c0065f..3e7d9fb 100644 --- a/properties.json +++ b/properties.json @@ -2072,6 +2072,30 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_33-1": { + "models": "ILX:0793734", + "name": "Myenteric ganglion", + "type": "ganglion", + "class": "auto-hide" + }, + "ganglion_34-1": { + "models": "ILX:0795343", + "name": "myenteric nerve plexus ganglion of esophagus", + "type": "ganglion", + "class": "auto-hide" + }, + "ganglion_35-1": { + "models": "ILX:0795350", + "name": "submucosal nerve plexus ganglion of rectum", + "type": "ganglion", + "class": "auto-hide" + }, + "ganglion_36-1": { + "models": "ILX:0795351", + "name": "submucosal nerve plexus ganglion of anus", + "type": "ganglion", + "class": "auto-hide" + }, "body_6-1": { "class": "body_6" }, @@ -2635,6 +2659,30 @@ "digestive_103-1": { "class": "digestive_103" }, + "digestive_104-1": { + "class": "digestive_104" + }, + "digestive_105-1": { + "class": "digestive_105" + }, + "digestive_106-1": { + "class": "digestive_106" + }, + "digestive_107-1": { + "class": "digestive_107" + }, + "digestive_108-1": { + "class": "digestive_108" + }, + "digestive_109-1": { + "class": "digestive_109" + }, + "digestive_110-1": { + "class": "digestive_110" + }, + "digestive_111-1": { + "class": "digestive_111" + }, "endocrine_1-1": { "class": "endocrine_1" }, @@ -3635,6 +3683,30 @@ "name": "periarterial neural plexus of the common hepatic artery", "type": "ganglion", "class": "auto-hide" + }}, + "plexus_21-1": { + "models": "UBERON:8410063", + "name": "myenteric nerve plexus of small intestine", + "type": "ganglion", + "class": "auto-hide" + }, + "plexus_22-1": { + "models": "ILX:0795346", + "name": "myenteric nerve plexus ganglion of rectum", + "type": "ganglion", + "class": "auto-hide" + }, + "plexus_23-1": { + "models": "ILX:0795347", + "name": "myenteric nerve plexus ganglion of anus", + "type": "ganglion", + "class": "auto-hide" + }, + "plexus_24-1": { + "models": "ILX:0793704", + "name": "Esophageal nerve plexus", + "type": "ganglion", + "class": "auto-hide" }, "label_5-1": { "class": "label_5" diff --git a/proxy_features.json b/proxy_features.json index 3f279a6..6935695 100644 --- a/proxy_features.json +++ b/proxy_features.json @@ -26,5 +26,12 @@ "proxies": [ "ILX:0786747" ] + }, + { + "feature": "UBERON:0002014", + "name": "inferior hypogastric nerve plexus", + "proxies": [ + "UBERON:0016508" + ] } ] From c14d2bfa209fb9715c7d0596d37b291f3c40f5b4 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 12:16:47 +1300 Subject: [PATCH 16/26] Add trigeminal, penile cavernous, and cardiac interganglionic nerves. --- cat_flatmap.svg | 9 +++++++++ properties.json | 12 ++++++++++++ 2 files changed, 21 insertions(+) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 4b737cf..74610a0 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -23060,6 +23060,15 @@ .id(nasopalatine_c) + + .id(trigeminal_c) + + + .id(penile_cavernous_c) + + + .id(cardiac_interganglionic_c) + \ No newline at end of file diff --git a/properties.json b/properties.json index 3e7d9fb..47db4f0 100644 --- a/properties.json +++ b/properties.json @@ -4174,6 +4174,18 @@ "type": "nerve", "models": "UBERON:0008810" }, + "trigeminal_c": { + "type": "nerve", + "models": "UBERON:0001645" + }, + "penile_cavernous_c": { + "type": "nerve", + "models": "ILX:0793807" + }, + "cardiac_interganglionic_c": { + "type": "nerve", + "models": "ILX:0796679" + }, "superior_laryngeal_19": { "type": "nerve" }, From 18d1262746afdea89af8a2d50a4b620d15c2f736 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 12:19:24 +1300 Subject: [PATCH 17/26] Add nerve plexus along the left precaval vein. --- cat_flatmap.svg | 3 +++ properties.json | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 74610a0..6f80c69 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -21041,6 +21041,9 @@ .id(plexus_24-1) + + .id(plexus_25-1) + Nodes diff --git a/properties.json b/properties.json index 47db4f0..9a8ebef 100644 --- a/properties.json +++ b/properties.json @@ -3708,6 +3708,12 @@ "type": "ganglion", "class": "auto-hide" }, + "plexus_25-1": { + "models": "ILX:0797430", + "name": "nerve plexus along the left precaval vein", + "type": "ganglion", + "class": "auto-hide" + }, "label_5-1": { "class": "label_5" }, From 3ee88eb7fffc5e9f96f8edbbda2ce70d70848f07 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 12:35:37 +1300 Subject: [PATCH 18/26] Fix incorrect syntax in properties.json. --- properties.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/properties.json b/properties.json index 9a8ebef..35d4957 100644 --- a/properties.json +++ b/properties.json @@ -3683,7 +3683,7 @@ "name": "periarterial neural plexus of the common hepatic artery", "type": "ganglion", "class": "auto-hide" - }}, + }, "plexus_21-1": { "models": "UBERON:8410063", "name": "myenteric nerve plexus of small intestine", From 6a3e1b2b09755535684cd38110863a91f8579285 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 14:40:49 +1300 Subject: [PATCH 19/26] Reorganise aliases and dots around prostate gland. --- anatomical_map.json | 4 ++++ cat_flatmap.svg | 53 +++++++---------------------------------- connectivity_terms.json | 32 +------------------------ properties.json | 9 +++---- 4 files changed, 17 insertions(+), 81 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index 320561c..535dd4e 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -887,6 +887,10 @@ "term": "UBERON:0002493", "name": "Uterine artery" }, + "reproductive_32": { + "term": "UBERON:0004713", + "name": "Corpus cavernosum penis" + }, "muscle_1": { "term": "ILX:0738319", "name": "T1-T2 intercostal muscle" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 6f80c69..ba3748e 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -11335,41 +11335,6 @@ - - .id(cardio_27-1) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - .id(cardio_11-1) @@ -20114,7 +20079,7 @@ .id(cardio_24-1) - .id(cardio_25-1) + .id(cardio_27-1) .id(cardio_28-1) @@ -20403,6 +20368,9 @@ .id(reproductive_31-1) + + .id(reproductive_32-1) + respiratory_labels @@ -20798,13 +20766,13 @@ .id(digestive_108-1) - .id(digestive_109-1) + .id(digestive_111-1) .id(digestive_110-1) - .id(digestive_111-1) + .id(digestive_109-1) @@ -20977,9 +20945,6 @@ .id(plexus_1-1) - - .id(plexus_5-1) - .id(plexus_6-1) @@ -21039,10 +21004,10 @@ .id(plexus_23-1) - .id(plexus_24-1) + .id(plexus_5-1) - .id(plexus_25-1) + .id(plexus_24-1) @@ -23066,7 +23031,7 @@ .id(trigeminal_c) - + .id(penile_cavernous_c) diff --git a/connectivity_terms.json b/connectivity_terms.json index 3ea9837..f92f219 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -343,19 +343,6 @@ ] ] }, - { - "id": [ - "ILX:0793141", - [] - ], - "name": "urethral rhabdosphincter", - "aliases": [ - [ - "UBERON:0004917", - [] - ] - ] - }, { "id": [ "ILX:0786272", @@ -642,19 +629,6 @@ ] ] }, - { - "id": [ - "UBERON:0005303", - [] - ], - "name": "hypogastric nerve", - "aliases": [ - [ - "UBERON:0002014", - [] - ] - ] - }, { "id": [ "ILX:0793141", @@ -667,11 +641,7 @@ [] ], [ - "UBERON:0004713", - [] - ], - [ - "ILX:0793807", + "UBERON:0004917", [] ] ] diff --git a/properties.json b/properties.json index 35d4957..79fca04 100644 --- a/properties.json +++ b/properties.json @@ -2849,6 +2849,9 @@ "reproductive_31-1": { "class": "reproductive_31" }, + "reproductive_32-1": { + "class": "reproductive_32" + }, "respiratory_10-1": { "class": "respiratory_10" }, @@ -3703,12 +3706,6 @@ "class": "auto-hide" }, "plexus_24-1": { - "models": "ILX:0793704", - "name": "Esophageal nerve plexus", - "type": "ganglion", - "class": "auto-hide" - }, - "plexus_25-1": { "models": "ILX:0797430", "name": "nerve plexus along the left precaval vein", "type": "ganglion", From 576bf83cf4676ae5de4b23763c69a1d018cbe4df Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 15:32:24 +1300 Subject: [PATCH 20/26] Fix the position of wall of duodenum. --- cat_flatmap.svg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index ba3748e..cbce182 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20750,7 +20750,7 @@ .id(digestive_100-1) - + .id(digestive_95-1) From 121f4a691f379e98342c6d57d5871090b8b41803 Mon Sep 17 00:00:00 2001 From: napakalas Date: Fri, 27 Feb 2026 16:28:50 +1300 Subject: [PATCH 21/26] Add dots to render gastint:10, pain1:11, mmset4:3b. --- anatomical_map.json | 8 ++++++++ cat_flatmap.svg | 11 ++++++++++- properties.json | 9 +++++++++ 3 files changed, 27 insertions(+), 1 deletion(-) diff --git a/anatomical_map.json b/anatomical_map.json index 535dd4e..68970bb 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -763,6 +763,10 @@ "term": "UBERON:0015716", "name": "epithelium of rectum" }, + "digestive_112": { + "term": "UBERON:0002108", + "name": "small intestine" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" @@ -891,6 +895,10 @@ "term": "UBERON:0004713", "name": "Corpus cavernosum penis" }, + "reproductive_33": { + "term": "UBERON:0011183", + "name": "corpus spongiosum of penis" + }, "muscle_1": { "term": "ILX:0738319", "name": "T1-T2 intercostal muscle" diff --git a/cat_flatmap.svg b/cat_flatmap.svg index cbce182..cd81395 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20045,7 +20045,7 @@ .id(brain_59-1) - .id(brain_50-1) + .id(brain_60-1) @@ -20255,6 +20255,9 @@ .id(digestive_92-1) + + .id(digestive_112-1) + Blue @@ -20371,6 +20374,9 @@ .id(reproductive_32-1) + + .id(reproductive_33-1) + respiratory_labels @@ -20774,6 +20780,9 @@ .id(digestive_109-1) + + .id(digestive_13-1) + Ganglia diff --git a/properties.json b/properties.json index 79fca04..fcdd15f 100644 --- a/properties.json +++ b/properties.json @@ -2401,6 +2401,9 @@ "digestive_12-1": { "class": "digestive_12" }, + "digestive_13-1": { + "class": "digestive_13" + }, "digestive_17-1": { "class": "digestive_17" }, @@ -2683,6 +2686,9 @@ "digestive_111-1": { "class": "digestive_111" }, + "digestive_112-1": { + "class": "digestive_112" + }, "endocrine_1-1": { "class": "endocrine_1" }, @@ -2852,6 +2858,9 @@ "reproductive_32-1": { "class": "reproductive_32" }, + "reproductive_33-1": { + "class": "reproductive_33" + }, "respiratory_10-1": { "class": "respiratory_10" }, From b3b7a8e4b4afa363331d598023e075ec6f2ce5e6 Mon Sep 17 00:00:00 2001 From: napakalas Date: Mon, 2 Mar 2026 09:59:38 +1300 Subject: [PATCH 22/26] Add an alias of intermediolateral nucleus of first thoracic segment. --- connectivity_terms.json | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/connectivity_terms.json b/connectivity_terms.json index f92f219..e928d08 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1601,6 +1601,10 @@ [ "ILX:0792474", [] + ], + [ + "ILX:0795493", + [] ] ] }, From 911cff875afc768d7bdabe434793bae70c2abbca Mon Sep 17 00:00:00 2001 From: napakalas Date: Wed, 4 Mar 2026 12:53:49 +1300 Subject: [PATCH 23/26] Fix incorrect draw of ganglion. --- cat_flatmap.svg | 12 ++++++------ properties.json | 24 ++++++++++++------------ 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index cd81395..b6ac8ac 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20948,6 +20948,12 @@ .id(ganglion_36-1) + + .id(ganglion_37-1) + + + .id(ganglion_38-1) + Plexus @@ -21006,12 +21012,6 @@ .id(plexus_21-1) - - .id(plexus_22-1) - - - .id(plexus_23-1) - .id(plexus_5-1) diff --git a/properties.json b/properties.json index fcdd15f..d611a42 100644 --- a/properties.json +++ b/properties.json @@ -2096,6 +2096,18 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_37-1": { + "models": "ILX:0795346", + "name": "myenteric nerve plexus ganglion of rectum", + "type": "ganglion", + "class": "auto-hide" + }, + "ganglion_38-1": { + "models": "ILX:0795347", + "name": "myenteric nerve plexus ganglion of anus", + "type": "ganglion", + "class": "auto-hide" + }, "body_6-1": { "class": "body_6" }, @@ -3702,18 +3714,6 @@ "type": "ganglion", "class": "auto-hide" }, - "plexus_22-1": { - "models": "ILX:0795346", - "name": "myenteric nerve plexus ganglion of rectum", - "type": "ganglion", - "class": "auto-hide" - }, - "plexus_23-1": { - "models": "ILX:0795347", - "name": "myenteric nerve plexus ganglion of anus", - "type": "ganglion", - "class": "auto-hide" - }, "plexus_24-1": { "models": "ILX:0797430", "name": "nerve plexus along the left precaval vein", From 253cfbea9ff68212c9388011ad933e7f694afdaf Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 5 Mar 2026 11:31:49 +1300 Subject: [PATCH 24/26] Remove unused dots in the svg file. --- anatomical_map.json | 4 ++-- cat_flatmap.svg | 55 ++------------------------------------------- 2 files changed, 4 insertions(+), 55 deletions(-) diff --git a/anatomical_map.json b/anatomical_map.json index 68970bb..7c4acf2 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -564,8 +564,8 @@ "name": "Red Pulp of Spleen" }, "digestive_62": { - "term": "UBERON:0001251", - "name": "Marginal Zone of Spleen" + "term": "ILX:0793681", + "name": "Marginal zone network" }, "digestive_63": { "term": "UBERON:0001960", diff --git a/cat_flatmap.svg b/cat_flatmap.svg index b6ac8ac..55afbd5 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20057,31 +20057,19 @@ .id(cardio_3-1) - - .id(cardio_18-1) - .id(cardio_19-1) - - .id(cardio_20-1) - .id(cardio_21-1) - - .id(cardio_22-1) - - - .id(cardio_23-1) - .id(cardio_24-1) .id(cardio_27-1) - + .id(cardio_28-1) @@ -20096,7 +20084,7 @@ .id(cardio_29-1) - + .id(cardio_29-2) @@ -20105,15 +20093,6 @@ .id(cardio_29-4) - - .id(cardio_31-1) - - - .id(cardio_33-1) - - - .id(cardio_34-1) - .id(cardio_35-1) @@ -20551,9 +20530,6 @@ .id(urinary_9-1) - - .id(urinary_10-1) - .id(urinary_11-1) @@ -20666,33 +20642,6 @@ - - .id(label_5-1) - - - .id(label_7-1) - - - .id(label_8-1) - - - .id(label_9-1) - - - .id(label_10-1) - - - .id(label_11-1) - - - .id(label_12-1) - - - .id(label_13-1) - - - .id(label_23-1) - .id(body_10-1) From a58e0136135cbe4bd07cb8c408e9f3b101332825 Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 5 Mar 2026 11:37:07 +1300 Subject: [PATCH 25/26] Remove unused ganglia and plexuses. --- cat_flatmap.svg | 17 +---------------- 1 file changed, 1 insertion(+), 16 deletions(-) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index 55afbd5..b1824d4 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20018,7 +20018,7 @@ .id(brain_34-1) - .id(brain_44-1) + .id(brain_56-1) .id(brain_45-1) @@ -20032,9 +20032,6 @@ .id(brain_55-1) - - .id(brain_56-1) - .id(brain_57-1) @@ -20822,9 +20819,6 @@ .id(ganglion_5-1) - - .id(ganglion_8-1) - .id(ganglion_9-1) @@ -20873,9 +20867,6 @@ .id(ganglion_25-1) - - .id(ganglion_26-1) - .id(ganglion_27-1) @@ -20909,9 +20900,6 @@ .id(plexus_1-1) - - .id(plexus_6-1) - .id(plexus_7-1) @@ -20940,9 +20928,6 @@ .id(plexus_14-1) - - .id(plexus_15-1) - .id(plexus_16-1) From 04e5498ca2b2c1bcf49832b8e9f688293879691e Mon Sep 17 00:00:00 2001 From: napakalas Date: Thu, 5 Mar 2026 14:26:19 +1300 Subject: [PATCH 26/26] Remove unused aliases. --- cat_flatmap.svg | 2 +- connectivity_terms.json | 70 ----------------------------------------- properties.json | 3 ++ 3 files changed, 4 insertions(+), 71 deletions(-) diff --git a/cat_flatmap.svg b/cat_flatmap.svg index b1824d4..0ee25ab 100644 --- a/cat_flatmap.svg +++ b/cat_flatmap.svg @@ -20094,7 +20094,7 @@ .id(cardio_35-1) - .id(cardio_35-2) + .id(cardio_16-1) .id(cardio_36-1) diff --git a/connectivity_terms.json b/connectivity_terms.json index e928d08..a990692 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -1,21 +1,4 @@ [ - { - "id": [ - "UBERON:0007240", - [ - "UBERON:0000947" - ] - ], - "name": "tunica adventitia of artery/aorta", - "aliases": [ - [ - "UBERON:0007240", - [ - "UBERON:0001496" - ] - ] - ] - }, { "id": [ "ILX:0793234", @@ -23,10 +6,6 @@ ], "name": "interganglionic branch of inferior cervical ganglion to middle cervical ganglion", "aliases": [ - [ - "ILX:0793363", - [] - ], [ "ILX:0739241", [] @@ -126,10 +105,6 @@ [ "ILX:0795013", [] - ], - [ - "ILX:0795017", - [] ] ] }, @@ -230,14 +205,6 @@ "UBERON:0001182" ] ], - [ - "ILX:0795012", - [] - ], - [ - "ILX:0795014", - [] - ], [ "UBERON:0018676", [] @@ -1295,10 +1262,6 @@ [ "ILX:0786788", [] - ], - [ - "ILX:0785947", - [] ] ] }, @@ -1393,10 +1356,6 @@ [ "ILX:0786477", [] - ], - [ - "ILX:0787285", - [] ] ] }, @@ -1509,10 +1468,6 @@ [ "UBERON:0001279", [] - ], - [ - "CL:1000488", - [] ] ] }, @@ -1539,10 +1494,6 @@ "UBERON:0001172", [] ], - [ - "CL:0000182", - [] - ], [ "ILX:0795016", [] @@ -1598,10 +1549,6 @@ ], "name": "T1 segment of thoracic spinal cord", "aliases": [ - [ - "ILX:0792474", - [] - ], [ "ILX:0795493", [] @@ -1704,10 +1651,6 @@ "ILX:0795042", [] ], - [ - "ILX:0795048", - [] - ], [ "ILX:0795040", [] @@ -1751,19 +1694,6 @@ ] ] }, - { - "id": [ - "ILX:0786163", - [] - ], - "name": "ventral root of the eighth cervical spinal cord segment", - "aliases": [ - [ - "UBERON:0014634", - [] - ] - ] - }, { "id": [ "UBERON:0001184", diff --git a/properties.json b/properties.json index d611a42..972c2c9 100644 --- a/properties.json +++ b/properties.json @@ -2305,6 +2305,9 @@ "cardio_13-1": { "class": "cardio_13" }, + "cardio_16-1": { + "class": "cardio_16" + }, "cardio_18-1": { "class": "cardio_18" },