diff --git a/anatomical_map.json b/anatomical_map.json index 7475cef..266be16 100644 --- a/anatomical_map.json +++ b/anatomical_map.json @@ -647,10 +647,6 @@ "term": "UBERON:0001832", "name": "Sublingual gland" }, - "digestive_82": { - "term": "UBERON:0002059", - "name": "Submandibular ganglion" - }, "digestive_83": { "term": "UBERON:0000006", "name": "Islet of langerhans" @@ -751,6 +747,26 @@ "term": "UBERON:0015716", "name": "epithelium of rectum" }, + "digestive_108": { + "term": "UBERON:0001182", + "name": "superior mesenteric artery" + }, + "digestive_109": { + "term": "UBERON:0006637", + "name": "celiac trunk" + }, + "digestive_110": { + "term": "ILX:0793739", + "name": "Nerve fiber from submandibular ganglion to sublingual gland" + }, + "digestive_111": { + "term": "ILX:0793737", + "name": "Nerve fiber from submandibular ganglion to submandibular gland" + }, + "digestive_112": { + "term": "ILX:0793738", + "name": "Nerve fiber from submandibular ganglion to mouth mucosa" + }, "reproductive_1": { "term": "UBERON:0000995", "name": "uterus" @@ -824,8 +840,8 @@ "name": "Epithelium of Vagina" }, "reproductive_19": { - "term": "UBERON:0009853", - "name": "Body of Uterus" + "term": "ILX:0794769", + "name": "Upper uterine segment" }, "reproductive_20": { "term": "UBERON:0001981", @@ -875,6 +891,38 @@ "term": "UBERON:0004713", "name": "Corpus cavernosum penis" }, + "reproductive_32": { + "term": "ILX:0794767", + "name": "smooth muscle of the upper uterus" + }, + "reproductive_33": { + "term": "ILX:0794765", + "name": "blood vessel of the upper uterus" + }, + "reproductive_34": { + "term": "ILX:0794770", + "name": "lower uterine segment" + }, + "reproductive_35": { + "term": "ILX:0794768", + "name": "smooth muscle of the lower uterus" + }, + "reproductive_36": { + "term": "ILX:0794766", + "name": "blood vessel of the lower uterus" + }, + "reproductive_37": { + "term": "ILX:0794731", + "name": "smooth muscle of the cervix" + }, + "reproductive_38": { + "term": "ILX:0794738", + "name": "blood vessel of the cervix" + }, + "reproductive_39": { + "term": "UBERON:0011183", + "name": "corpus spongiosum of penis" + }, "muscle_1": { "term": "ILX:0738319", "name": "T1-T2 intercostal muscle" diff --git a/connectivity_terms.json b/connectivity_terms.json index 5906916..a9c2bf4 100644 --- a/connectivity_terms.json +++ b/connectivity_terms.json @@ -12,19 +12,6 @@ ] ] }, - { - "id": [ - "ILX:0793233", - [] - ], - "name": "interganglionic branch of inferior cervical ganglion to first thoracic ganglion/sympathetic trunk", - "aliases": [ - [ - "ILX:0738291", - [] - ] - ] - }, { "id": [ "ILX:0793234", @@ -171,10 +158,6 @@ "UBERON:0005488", [] ], - [ - "ILX:0794732", - [] - ], [ "UBERON:0035772", [] @@ -195,26 +178,10 @@ "UBERON:0002010", [] ], - [ - "UBERON:0005734", - [ - "UBERON:0006637" - ] - ], - [ - "UBERON:0005734", - [ - "UBERON:0001182" - ] - ], [ "UBERON:0018676", [] ], - [ - "UBERON:0011926", - [] - ], [ "ILX:0795513", [] @@ -284,21 +251,6 @@ ] ] }, - { - "id": [ - "UBERON:0005364", - [ - "UBERON:0005363" - ] - ], - "name": "", - "aliases": [ - [ - "UBERON:0003535", - [] - ] - ] - }, { "id": [ "UBERON:0016580", @@ -321,42 +273,12 @@ ], "name": "urethral rhabdosphincter", "aliases": [ - [ - "UBERON:0004917", - [] - ], [ "UBERON:0011380", [] ] ] }, - { - "id": [ - "ILX:0786272", - [] - ], - "name": "", - "aliases": [ - [ - "ILX:0793619", - [] - ] - ] - }, - { - "id": [ - "ILX:0786722", - [] - ], - "name": "", - "aliases": [ - [ - "ILX:0793618", - [] - ] - ] - }, { "id": [ "UBERON:0006458", @@ -370,45 +292,6 @@ ] ] }, - { - "id": [ - "ILX:0786141", - [] - ], - "name": "Fifth thoracic ganglion ", - "aliases": [ - [ - "ILX:0793335", - [] - ] - ] - }, - { - "id": [ - "ILX:0789947", - [] - ], - "name": "Sixth thoracic ganglion", - "aliases": [ - [ - "ILX:0793336", - [] - ] - ] - }, - { - "id": [ - "ILX:0786228", - [] - ], - "name": "Second thoracic ganglion", - "aliases": [ - [ - "ILX:0793617", - [] - ] - ] - }, { "id": [ "UBERON:0006459", @@ -422,19 +305,6 @@ ] ] }, - { - "id": [ - "ILX:0793233", - [] - ], - "name": "", - "aliases": [ - [ - "UBERON:0002441", - [] - ] - ] - }, { "id": [ "UBERON:0006452", @@ -534,19 +404,6 @@ ] ] }, - { - "id": [ - "UBERON:0005303", - [] - ], - "name": "hypogastric nerve", - "aliases": [ - [ - "ILX:0793803", - [] - ] - ] - }, { "id": [ "UBERON:0000992", @@ -625,18 +482,9 @@ [ "ILX:0793884", [] - ] - ] - }, - { - "id": [ - "UBERON:0000057", - [] - ], - "name": "urethra", - "aliases": [ + ], [ - "UBERON:0011183", + "ILX:0793803", [] ] ] @@ -723,19 +571,6 @@ ] ] }, - { - "id": [ - "UBERON:0005453", - [] - ], - "name": "inferior mesenteric ganglion", - "aliases": [ - [ - "UBERON:0035770", - [] - ] - ] - }, { "id": [ "UBERON:0002367", @@ -806,10 +641,6 @@ [ "ILX:0793817", [] - ], - [ - "UBERON:0007715", - [] ] ] }, @@ -836,10 +667,6 @@ [ "ILX:0793818", [] - ], - [ - "UBERON:0007716", - [] ] ] }, @@ -873,53 +700,6 @@ ] ] }, - { - "id": [ - "UBERON:0009853", - [] - ], - "name": "body of uterus", - "aliases": [ - [ - "ILX:0794769", - [] - ], - [ - "ILX:0794767", - [] - ] - ] - }, - { - "id": [ - "UBERON:0000002", - [] - ], - "name": "uterine cervix", - "aliases": [ - [ - "ILX:0794770", - [] - ], - [ - "ILX:0794768", - [] - ] - ] - }, - { - "id": [ - "UBERON:0004223", - [] - ], - "name": "smooth muscle/vagina", - "aliases": [ - [ - "ILX:0794731", - [] - ] - ] - }, { "id": [ "UBERON:0001981", @@ -946,50 +726,12 @@ "UBERON:0006608", [] ], - [ - "ILX:0793809", - [] - ], [ "UBERON:0008323", [] ] ] }, - { - "id": [ - "UBERON:0001981", - [ - "UBERON:0000002" - ] - ], - "name": "blood vessel/uterine cervix", - "aliases": [ - [ - "ILX:0794738", - [] - ], - [ - "ILX:0794766", - [] - ] - ] - }, - { - "id": [ - "UBERON:0001981", - [ - "UBERON:0009853" - ] - ], - "name": "blood vessel/body of uterus", - "aliases": [ - [ - "ILX:0794765", - [] - ] - ] - }, { "id": [ "UBERON:0006463", @@ -1035,45 +777,6 @@ ] ] }, - { - "id": [ - "ILX:0793832", - [] - ], - "name": "Ovarian Nerve Plexus", - "aliases": [ - [ - "ILX:0793822", - [] - ] - ] - }, - { - "id": [ - "UBERON:0001736", - [] - ], - "name": "submandibular gland", - "aliases": [ - [ - "ILX:0793737", - [] - ] - ] - }, - { - "id": [ - "UBERON:0001832", - [] - ], - "name": "sublingual gland", - "aliases": [ - [ - "ILX:0793739", - [] - ] - ] - }, { "id": [ "UBERON:0001723", @@ -1081,17 +784,9 @@ ], "name": "tongue", "aliases": [ - [ - "UBERON:0003721", - [] - ], [ "UBERON:0003729", [] - ], - [ - "ILX:0793738", - [] ] ] }, @@ -1479,10 +1174,6 @@ [ "UBERON:0004820", [] - ], - [ - "UBERON:0001279", - [] ] ] }, @@ -1520,6 +1211,10 @@ [ "UBERON:0015423", [] + ], + [ + "UBERON:0001279", + [] ] ] }, @@ -1612,82 +1307,9 @@ [ "ILX:0794853", [] - ] - ] - }, - { - "id": [ - "UBERON:0006118", - [] - ], - "name": "lamina I of gray matter of spinal cord", - "aliases": [ - [ - "ILX:0795026", - [] - ], - [ - "ILX:0795027", - [] - ], - [ - "ILX:0795028", - [] ], [ - "ILX:0795029", - [] - ], - [ - "ILX:0795030", - [] - ], - [ - "ILX:0795045", - [] - ], - [ - "ILX:0795041", - [] - ], - [ - "ILX:0795046", - [] - ], - [ - "ILX:0795043", - [] - ], - [ - "ILX:0795047", - [] - ], - [ - "ILX:0795042", - [] - ], - [ - "ILX:0795040", - [] - ], - [ - "ILX:0795023", - [] - ], - [ - "ILX:0795024", - [] - ], - [ - "ILX:0795025", - [] - ], - [ - "ILX:0795031", - [] - ], - [ - "ILX:0795044", + "UBERON:0003535", [] ] ] @@ -2005,6 +1627,21 @@ ] ] }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006454" + ] + ], + "name": "gray matter of spinal cord/sixth thoracic spinal cord segment", + "aliases": [ + [ + "ILX:0795040", + [] + ] + ] + }, { "id": [ "UBERON:0002315", @@ -2017,6 +1654,14 @@ [ "ILX:0796498", [] + ], + [ + "ILX:0795041", + [] + ], + [ + "ILX:0795023", + [] ] ] }, @@ -2032,6 +1677,14 @@ [ "ILX:0795032", [] + ], + [ + "ILX:0795042", + [] + ], + [ + "ILX:0795024", + [] ] ] }, @@ -2047,6 +1700,14 @@ [ "ILX:0795033", [] + ], + [ + "ILX:0795043", + [] + ], + [ + "ILX:0795025", + [] ] ] }, @@ -2062,6 +1723,14 @@ [ "ILX:0795034", [] + ], + [ + "ILX:0795026", + [] + ], + [ + "ILX:0795044", + [] ] ] }, @@ -2077,6 +1746,14 @@ [ "ILX:0795035", [] + ], + [ + "ILX:0795027", + [] + ], + [ + "ILX:0795045", + [] ] ] }, @@ -2092,6 +1769,14 @@ [ "ILX:0795036", [] + ], + [ + "ILX:0795028", + [] + ], + [ + "ILX:0795046", + [] ] ] }, @@ -2107,6 +1792,10 @@ [ "ILX:0795037", [] + ], + [ + "ILX:0795047", + [] ] ] }, @@ -2122,6 +1811,10 @@ [ "ILX:0795038", [] + ], + [ + "ILX:0795029", + [] ] ] }, @@ -2137,6 +1830,25 @@ [ "ILX:0795039", [] + ], + [ + "ILX:0795030", + [] + ] + ] + }, + { + "id": [ + "UBERON:0002315", + [ + "UBERON:0006449" + ] + ], + "name": "gray matter of spinal cord/third lumbar spinal cord segment", + "aliases": [ + [ + "ILX:0795031", + [] ] ] }, diff --git a/properties.json b/properties.json index d16e53f..77ddeac 100644 --- a/properties.json +++ b/properties.json @@ -1770,133 +1770,128 @@ "name": "Gray communicating ramus of fourth sacral nerve" }, "S50_C1": { - "class": "spinal_50" + "models": "ILX:0788141", + "name": "First cervical nerve" }, "S50_C2": { - "class": "spinal_50" + "models": "ILX:0785476", + "name": "Second cervical nerve" }, "S50_C3": { - "class": "spinal_50" + "models": "ILX:0790034", + "name": "Third cervical nerve" }, "S50_C4": { - "class": "spinal_50" + "models": "ILX:0792861", + "name": "Fourth cervical nerve" }, "S50_C5": { - "class": "spinal_50" + "models": "ILX:0791493", + "name": "Fifth cervical nerve" }, "S50_C6": { - "class": "spinal_50" + "models": "ILX:0787473", + "name": "Sixth cervical nerve" }, "S50_C7": { - "class": "spinal_50" + "models": "ILX:0789608", + "name": "Seventh cervical nerve" }, "S50_C8": { - "class": "spinal_50" + "models": "UBERON:0000962", + "name": "Eighth cervical nerve" }, "S50_L1": { - "class": "spinal_50" - }, - "S50_L1-1": { "models": "ILX:0788972", "name": "First lumbar nerve" }, "S50_L2": { - "class": "spinal_50" - }, - "S50_L2-1": { "models": "ILX:0786362", "name": "Second lumbar nerve" }, "S50_L3": { - "class": "spinal_50" - }, - "S50_L3-1": { "models": "ILX:0789374", "name": "Third lumbar nerve" }, "S50_L4": { - "class": "spinal_50" - }, - "S50_L4-1": { "models": "ILX:0788896", "name": "Fourth lumbar nerve" }, "S50_L5": { - "class": "spinal_50" + "models": "ILX:0787261", + "name": "Fifth lumbar nerve" }, "S50_L6": { - "class": "spinal_50" + "models": "UBERON:0009624", + "name": "Sixth lumbar nerve" }, "S50_S1": { - "class": "spinal_50" - }, - "S50_S1-1": { "models": "ILX:0790504", "name": "First sacral nerve" }, "S50_S2": { - "class": "spinal_50" - }, - "S50_S2-1": { "models": "ILX:0787528", "name": "Second sacral nerve" }, "S50_S3": { - "class": "spinal_50" - }, - "S50_S3-1": { "models": "ILX:0791971", "name": "Third sacral nerve" }, "S50_S4": { - "class": "spinal_50" - }, - "S50_S4-1": { "models": "ILX:0792327", "name": "Fourth sacral nerve" }, "S50_T1": { - "class": "spinal_50" + "models": "ILX:0738397", + "name": "First thoracic nerve" }, "S50_T2": { - "class": "spinal_50" + "models": "ILX:0739243", + "name": "Second thoracic nerve" }, "S50_T3": { - "class": "spinal_50" + "models": "ILX:0739246", + "name": "Third thoracic nerve" }, "S50_T4": { - "class": "spinal_50" + "models": "ILX:0784755", + "name": "Fourth thoracic nerve" }, "S50_T5": { - "class": "spinal_50" + "models": "ILX:0792589", + "name": "Fifth thoracic nerve" }, "S50_T6": { - "class": "spinal_50" + "models": "ILX:0791122", + "name": "Sixth thoracic nerve" }, "S50_T7": { - "class": "spinal_50" + "models": "ILX:0789008", + "name": "Seventh thoracic nerve" }, "S50_T8": { - "class": "spinal_50" + "models": "ILX:0792754", + "name": "Eighth thoracic nerve" }, "S50_T9": { - "class": "spinal_50" + "models": "ILX:0789545", + "name": "Ninth thoracic nerve" }, "S50_T10": { - "class": "spinal_50" + "models": "ILX:0792933", + "name": "Tenth thoracic nerve" }, "S50_T11": { - "class": "spinal_50" + "models": "ILX:0791454", + "name": "Eleventh thoracic nerve" }, "S50_T12": { - "class": "spinal_50" - }, - "S50_T12-1": { "models": "ILX:0791046", "name": "Twelfth thoracic nerve" }, "S50_T13": { - "class": "spinal_50" + "models": "UBERON:0003726", + "name": "Thirteenth thoracic nerve" }, "S51_L6": { "class": "spinal_51" @@ -2108,6 +2103,12 @@ "type": "ganglion", "class": "auto-hide" }, + "ganglion_39-1": { + "models": "UBERON:0002059", + "name": "Submandibular ganglion", + "type": "ganglion", + "class": "auto-hide" + }, "body_1-1": { "class": "body_1" }, @@ -2567,15 +2568,9 @@ "digestive_71-1": { "class": "digestive_71" }, - "digestive_71-2": { - "class": "digestive_71" - }, "digestive_72-1": { "class": "digestive_72" }, - "digestive_72-2": { - "class": "digestive_72" - }, "digestive_73-1": { "class": "digestive_73" }, @@ -2606,9 +2601,6 @@ "digestive_81-1": { "class": "digestive_81" }, - "digestive_82-1": { - "class": "digestive_82" - }, "digestive_83-1": { "class": "digestive_83" }, @@ -2687,6 +2679,21 @@ "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" + }, + "digestive_112-1": { + "class": "digestive_112" + }, "endocrine_2-1": { "class": "endocrine_2" }, @@ -2871,6 +2878,30 @@ "reproductive_31-1": { "class": "reproductive_31" }, + "reproductive_32-1": { + "class": "reproductive_32" + }, + "reproductive_33-1": { + "class": "reproductive_33" + }, + "reproductive_34-1": { + "class": "reproductive_34" + }, + "reproductive_35-1": { + "class": "reproductive_35" + }, + "reproductive_36-1": { + "class": "reproductive_36" + }, + "reproductive_37-1": { + "class": "reproductive_37" + }, + "reproductive_38-1": { + "class": "reproductive_38" + }, + "reproductive_39-1": { + "class": "reproductive_39" + }, "respiratory_10-1": { "class": "respiratory_10" }, @@ -3721,6 +3752,12 @@ "type": "ganglion", "class": "auto-hide" }, + "plexus_26-1": { + "models": "ILX:0794732", + "name": "intermesenteric plexus", + "type": "ganglion", + "class": "auto-hide" + }, "label_4-1": { "class": "label_4" }, @@ -4145,7 +4182,7 @@ }, "ICG-T1_sympathetic_cord_c": { "type": "nerve", - "models": "ILX:0793233" + "models": "ILX:0738291" }, "MCG-ICG_sympathetic_cord_c": { "type": "nerve", @@ -4211,6 +4248,18 @@ "type": "nerve", "models": "ILX:0796679" }, + "lingual_c": { + "type": "nerve", + "models": "UBERON:0003721" + }, + "clitoral_cavernous_c": { + "type": "nerve", + "models": "ILX:0793809" + }, + "superior_ovarian_nerve_c": { + "type": "nerve", + "models": "ILX:0793822" + }, "n_76_c": { "type": "nerve" }, @@ -5746,7 +5795,7 @@ }, { "id": "ICG-T1_sympathetic_cord", - "models": "ILX:0793233", + "models": "ILX:0738291", "connects": [ "ganglion_10-1", "S46_T1" diff --git a/proxy_features.json b/proxy_features.json index 6935695..e9e7d44 100644 --- a/proxy_features.json +++ b/proxy_features.json @@ -33,5 +33,82 @@ "proxies": [ "UBERON:0016508" ] + }, + { + "feature": "ILX:0793617", + "name": "T2 sympathetic chain", + "proxies": [ + "ILX:0786228" + ] + }, + { + "feature": "ILX:0793618", + "name": "T3 sympathetic chain", + "proxies": [ + "ILX:0786722" + ] + }, + { + "feature": "ILX:0793619", + "name": "T4 sympathetic chain", + "proxies": [ + "ILX:0786272" + ] + }, + { + "feature": "ILX:0793335", + "name": "T5 sympathetic chain", + "proxies": [ + "ILX:0786141" + ] + }, + { + "feature": "ILX:0793336", + "name": "T6 sympathetic chain", + "proxies": [ + "ILX:0789947" + ] + }, + { + "feature": "UBERON:0002441", + "name": "cervicothoracic ganglion", + "proxies": [ + "ILX:0774266" + ] + }, + { + "feature": "UBERON:0035770", + "name": "inferior mesenteric nerve plexus", + "proxies": [ + "UBERON:0005453" + ] + }, + { + "feature": "UBERON:0007715", + "name": "thoracic subsegment of spinal cord", + "proxies": [ + "ILX:0793357" + ] + }, + { + "feature": "UBERON:0007716", + "name": "lumbar subsegment of spinal cord", + "proxies": [ + "UBERON:0006448" + ] + }, + { + "feature": "UBERON:0004917", + "name": "urethral sphincter", + "proxies": [ + "ILX:0793141" + ] + }, + { + "feature": "UBERON:0001780", + "name": "spinal nerve", + "proxies": [ + "ILX:0738397" + ] } ] diff --git a/rat_flatmap.svg b/rat_flatmap.svg index 3568b8b..f58f450 100644 --- a/rat_flatmap.svg +++ b/rat_flatmap.svg @@ -718,69 +718,42 @@ .id(S50_T11) - - .id(S50_T12-1) - - .id(S50_T12) - - + + .id(S50_T12) + .id(S50_T13) - - .id(S50_L1-1) - - .id(S50_L1) - - - - .id(S50_L2-1) - - .id(S50_L2) - - - - .id(S50_L3-1) - - .id(S50_L3) - - - - .id(S50_L4-1) - - .id(S50_L4) - - + + .id(S50_L1) + + + .id(S50_L2) + + + .id(S50_L3) + + + .id(S50_L4) + .id(S50_L5) .id(S50_L6) - - .id(S50_S1-1) - - .id(S50_S1) - - - - .id(S50_S2-1) - - .id(S50_S2) - - - - .id(S50_S3-1) - - .id(S50_S3) - - - - .id(S50_S4-1) - - .id(S50_S4) - - + + .id(S50_S1) + + + .id(S50_S2) + + + .id(S50_S3) + + + .id(S50_S4) + dorsal_root_of_spinal_cord @@ -12478,27 +12451,42 @@ - - .id(reproductive_11-1) - .id(reproductive_12-1) .id(reproductive_13-1) - - .id(reproductive_19-1) - - - .id(reproductive_20-1) - .id(reproductive_23-1) - - .id(reproductive_20-3) - + + .id(reproductive_19-1) + + .id(reproductive_32-1) + + + .id(reproductive_33-1) + + + + .id(reproductive_34-1) + + .id(reproductive_35-1) + + + .id(reproductive_36-1) + + + + .id(reproductive_11-1) + + .id(reproductive_37-1) + + + .id(reproductive_38-1) + + .id(reproductive_25-1) @@ -14041,9 +14029,12 @@ - + .id(reproductive_31-1) + + .id(reproductive_39-1) + .id(reproductive_5-1) @@ -14278,9 +14269,6 @@ .id(digestive_59-1) - .id(digestive_71-2) - - .id(digestive_71-1) @@ -14292,10 +14280,10 @@ .id(digestive_61-1) - - .id(digestive_72-2) + + .id(digestive_102-1) - + .id(digestive_72-1) @@ -14624,8 +14612,8 @@ .id(body_10-1) - - .id(digestive_82-1) + + .id(ganglion_39-1) .id(label_24-1) @@ -14684,9 +14672,6 @@ .id(digestive_99-1) - - .id(digestive_102-1) - .id(digestive_103-1) @@ -14702,6 +14687,21 @@ .id(digestive_107-1) + + .id(digestive_108-1) + + + .id(digestive_109-1) + + + .id(digestive_110-1) + + + .id(digestive_111-1) + + + .id(digestive_112-1) + Nodes @@ -15353,9 +15353,6 @@ .id(S46_S4) - - .id(ganglion_1-1) - .id(ganglion_2-1) @@ -15494,6 +15491,9 @@ .id(plexus_25-1) + + .id(plexus_26-1) + Centerlines @@ -16736,6 +16736,15 @@ .id(cardiac_interganglionic_c) + + .id(clitoral_cavernous_c) + + + .id(lingual_c) + + + .id(superior_ovarian_nerve_c) +