diff --git a/aism-base.json b/aism-base.json
index fea9778..6cbfc63 100644
--- a/aism-base.json
+++ b/aism-base.json
@@ -40,9 +40,9 @@
"val" : "https://creativecommons.org/licenses/by/4.0/"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
- "val" : "2024-03-16"
+ "val" : "2024-05-11"
} ],
- "version" : "http://purl.obolibrary.org/obo/aism/releases/2024-03-16/aism-base.json"
+ "version" : "http://purl.obolibrary.org/obo/aism/releases/2024-05-11/aism-base.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/AISM_0000000",
@@ -2795,11 +2795,11 @@
"type" : "CLASS",
"meta" : {
"definition" : {
- "val" : "The anatomical space adjacent to two cuticular punctures."
+ "val" : "The distance between two cuticular punctures."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
- "val" : "Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188"
+ "val" : "Edited by jgiron https://orcid.org/0000-0002-0851-6883 \n2024-05-11\nTo make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'\nMatching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318\n\nFormer definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188"
} ]
}
}, {
diff --git a/aism-base.obo b/aism-base.obo
index 43ba039..c662822 100644
--- a/aism-base.obo
+++ b/aism-base.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: aism/releases/2024-03-16/aism-base.owl
+data-version: aism/releases/2024-05-11/aism-base.owl
ontology: aism/aism-base
property_value: http://purl.org/dc/elements/1.1/contributor "Giulio Montanaro (gmontanaro) https://orcid.org/0000-0003-0836-1364" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "István Mikó (imiko) https://orcid.org/0000-0003-2938-9075" xsd:string
@@ -13,7 +13,7 @@ property_value: http://purl.org/dc/terms/license https://creativecommons.org/lic
property_value: IAO:0000700 "http://purl.obolibrary.org/obo/AISM_0000174" xsd:string
property_value: IAO:0000700 "http://purl.obolibrary.org/obo/PATO_0000001" xsd:string
property_value: IAO:0000700 "http://purl.obolibrary.org/obo/UBERON_0001062" xsd:string
-property_value: owl:versionInfo "2024-03-16" xsd:string
+property_value: owl:versionInfo "2024-05-11" xsd:string
[Term]
id: AISM:0000000
@@ -2266,8 +2266,8 @@ relationship: parallel_to AISM:0000377 {http://purl.org/dc/elements/1.1/contribu
[Term]
id: AISM:0000376
name: interpunctural distance {creation_date="2023-06-04", IAO:0000232="Moved from COLAO to AISM: 2023-05-08\ngmontanaro https://orcid.org/0000-0003-0836-1364", http://purl.org/dc/elements/1.1/contributor="gmontanaro https://orcid.org/0000-0003-0836-1364"}
-def: "The anatomical space adjacent to two cuticular punctures." [] {creation_date="2023-06-04", http://purl.org/dc/elements/1.1/contributor="gmontanaro https://orcid.org/0000-0003-0836-1364"}
-property_value: IAO:0000232 "Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188" xsd:string {http://purl.org/dc/elements/1.1/contributor="jgiron https://orcid.org/0000-0002-0851-6883", creation_date="2024-02-14"}
+def: "The distance between two cuticular punctures." [] {creation_date="2023-06-04", http://purl.org/dc/elements/1.1/contributor="gmontanaro https://orcid.org/0000-0003-0836-1364"}
+property_value: IAO:0000232 "Edited by jgiron https://orcid.org/0000-0002-0851-6883 \n2024-05-11\nTo make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'\nMatching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318\n\nFormer definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188" xsd:string {http://purl.org/dc/elements/1.1/contributor="jgiron https://orcid.org/0000-0002-0851-6883", creation_date="2024-02-14"}
[Term]
id: AISM:0000377
diff --git a/aism-base.owl b/aism-base.owl
index 8662092..5c36acb 100644
--- a/aism-base.owl
+++ b/aism-base.owl
@@ -38,7 +38,7 @@
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"
xmlns:caloha-reqs-vetted="http://purl.obolibrary.org/obo/caloha-reqs-vetted#">
-
+
http://purl.obolibrary.org/obo/AISM_0000174
http://purl.obolibrary.org/obo/PATO_0000001
http://purl.obolibrary.org/obo/UBERON_0001062
@@ -51,7 +51,7 @@
Ontology for the Anatomy of the Insect SkeletoMuscular system
- 2024-03-16
+ 2024-05-11
@@ -17943,15 +17943,20 @@ gmontanaro https://orcid.org/0000-0003-0836-1364
- The anatomical space adjacent to two cuticular punctures.
- Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
+ The distance between two cuticular punctures.
+ Edited by jgiron https://orcid.org/0000-0002-0851-6883
+2024-05-11
+To make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'
+Matching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318
+
+Former definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
interpunctural distance
-
+
-
+
@@ -17966,14 +17971,19 @@ gmontanaro https://orcid.org/0000-0003-0836-1364
- The anatomical space adjacent to two cuticular punctures.
+ The distance between two cuticular punctures.
gmontanaro https://orcid.org/0000-0003-0836-1364
2023-06-04
- Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
+ Edited by jgiron https://orcid.org/0000-0002-0851-6883
+2024-05-11
+To make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'
+Matching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318
+
+Former definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
jgiron https://orcid.org/0000-0002-0851-6883
2024-02-14
@@ -45927,6 +45937,12 @@ starasov https://orcid.org/0000-0001-5237-2330
+
+
+
+
+
+
@@ -46137,12 +46153,6 @@ starasov https://orcid.org/0000-0001-5237-2330
-
-
-
-
-
-
diff --git a/aism-full.json b/aism-full.json
index 3d25b29..02f9145 100644
--- a/aism-full.json
+++ b/aism-full.json
@@ -37,9 +37,9 @@
"val" : "https://creativecommons.org/licenses/by/4.0/"
}, {
"pred" : "http://www.w3.org/2002/07/owl#versionInfo",
- "val" : "2024-03-16"
+ "val" : "2024-05-11"
} ],
- "version" : "http://purl.obolibrary.org/obo/aism/releases/2024-03-16/aism-full.json"
+ "version" : "http://purl.obolibrary.org/obo/aism/releases/2024-05-11/aism-full.json"
},
"nodes" : [ {
"id" : "http://purl.obolibrary.org/obo/IAO_0000002",
@@ -3161,11 +3161,11 @@
"type" : "CLASS",
"meta" : {
"definition" : {
- "val" : "The anatomical space adjacent to two cuticular punctures."
+ "val" : "The distance between two cuticular punctures."
},
"basicPropertyValues" : [ {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
- "val" : "Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188"
+ "val" : "Edited by jgiron https://orcid.org/0000-0002-0851-6883 \n2024-05-11\nTo make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'\nMatching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318\n\nFormer definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188"
} ]
}
}, {
@@ -158479,9 +158479,6 @@
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand",
"val" : "has_characteristic"
- }, {
- "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso",
- "val" : "https://github.com/oborel/obo-relations/pull/284"
} ]
}
}, {
@@ -164349,6 +164346,12 @@
}, {
"pred" : "http://purl.obolibrary.org/obo/IAO_0000232",
"val" : "See github ticket https://github.com/oborel/obo-relations/issues/497"
+ }, {
+ "pred" : "http://purl.org/dc/terms/contributor",
+ "val" : "https://orcid.org/0000-0001-9625-1899"
+ }, {
+ "pred" : "http://purl.org/dc/terms/contributor",
+ "val" : "https://orcid.org/0000-0003-2620-0345"
}, {
"pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date",
"val" : "2021-11-08T12:00:00Z"
@@ -305123,10 +305126,6 @@
"sub" : "http://purl.obolibrary.org/obo/GO_0008150",
"pred" : "is_a",
"obj" : "http://purl.obolibrary.org/obo/BFO_0000015"
- }, {
- "sub" : "http://purl.obolibrary.org/obo/GO_0008150",
- "pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
- "obj" : "http://purl.obolibrary.org/obo/GO_0003674"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0008152",
"pred" : "is_a",
@@ -315350,7 +315349,7 @@
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0042391",
"pred" : "is_a",
- "obj" : "http://purl.obolibrary.org/obo/BFO_0000015"
+ "obj" : "http://purl.obolibrary.org/obo/BFO_0000003"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0042391",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
@@ -332731,6 +332730,10 @@
"sub" : "http://purl.obolibrary.org/obo/GO_0099738",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000050",
"obj" : "http://purl.obolibrary.org/obo/GO_0005938"
+ }, {
+ "sub" : "http://purl.obolibrary.org/obo/GO_0100001",
+ "pred" : "is_a",
+ "obj" : "http://purl.obolibrary.org/obo/BFO_0000015"
}, {
"sub" : "http://purl.obolibrary.org/obo/GO_0100001",
"pred" : "is_a",
@@ -426416,10 +426419,6 @@
"sub" : "http://purl.obolibrary.org/obo/BFO_0000004",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000050",
"obj" : "http://purl.obolibrary.org/obo/BFO_0000004"
- }, {
- "sub" : "http://purl.obolibrary.org/obo/BFO_0000015",
- "pred" : "http://purl.obolibrary.org/obo/BFO_0000050",
- "obj" : "http://purl.obolibrary.org/obo/BFO_0000015"
}, {
"sub" : "http://purl.obolibrary.org/obo/BFO_0000017",
"pred" : "http://purl.obolibrary.org/obo/BFO_0000050",
@@ -426437,13 +426436,6 @@
"pred" : "http://purl.obolibrary.org/obo/BFO_0000050",
"obj" : "http://purl.obolibrary.org/obo/BFO_0000031"
} ]
- }, {
- "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000051",
- "allValuesFromEdges" : [ {
- "sub" : "http://purl.obolibrary.org/obo/BFO_0000020",
- "pred" : "http://purl.obolibrary.org/obo/BFO_0000051",
- "obj" : "http://purl.obolibrary.org/obo/BFO_0000020"
- } ]
}, {
"predicateId" : "http://purl.obolibrary.org/obo/RO_0002162",
"allValuesFromEdges" : [ {
@@ -426883,7 +426875,7 @@
"rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ]
}, {
"predicateId" : "http://purl.obolibrary.org/obo/RO_0000057",
- "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003", "http://purl.obolibrary.org/obo/BFO_0000015" ],
+ "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000003" ],
"rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ]
}, {
"predicateId" : "http://purl.obolibrary.org/obo/RO_0000079",
diff --git a/aism-full.obo b/aism-full.obo
index 53cc1b9..0a698fe 100644
--- a/aism-full.obo
+++ b/aism-full.obo
@@ -1,5 +1,5 @@
format-version: 1.2
-data-version: aism/releases/2024-03-16/aism-full.owl
+data-version: aism/releases/2024-05-11/aism-full.owl
subsetdef: 1_STAR ""
subsetdef: 2_STAR ""
subsetdef: 3_STAR ""
@@ -100,7 +100,7 @@ property_value: http://purl.org/dc/elements/1.1/contributor "István Mikó (imik
property_value: http://purl.org/dc/elements/1.1/contributor "Jennifer C. Girón (jgiron) https://orcid.org/0000-0002-0851-6883" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Luis A. González Montaña (lagonzalezmo) https://orcid.org/0000-0002-9136-9932" xsd:string
property_value: http://purl.org/dc/elements/1.1/contributor "Sergei Tarasov (starasov) https://orcid.org/0000-0001-5237-2330" xsd:string
-property_value: owl:versionInfo "2024-03-16" xsd:string
+property_value: owl:versionInfo "2024-05-11" xsd:string
[Term]
id: AISM:0000000
@@ -2353,8 +2353,8 @@ relationship: parallel_to AISM:0000377 {http://purl.org/dc/elements/1.1/contribu
[Term]
id: AISM:0000376
name: interpunctural distance {creation_date="2023-06-04", IAO:0000232="Moved from COLAO to AISM: 2023-05-08\ngmontanaro https://orcid.org/0000-0003-0836-1364", http://purl.org/dc/elements/1.1/contributor="gmontanaro https://orcid.org/0000-0003-0836-1364"}
-def: "The anatomical space adjacent to two cuticular punctures." [] {creation_date="2023-06-04", http://purl.org/dc/elements/1.1/contributor="gmontanaro https://orcid.org/0000-0003-0836-1364"}
-property_value: curator_notes "Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188" xsd:string {http://purl.org/dc/elements/1.1/contributor="jgiron https://orcid.org/0000-0002-0851-6883", creation_date="2024-02-14"}
+def: "The distance between two cuticular punctures." [] {creation_date="2023-06-04", http://purl.org/dc/elements/1.1/contributor="gmontanaro https://orcid.org/0000-0003-0836-1364"}
+property_value: curator_notes "Edited by jgiron https://orcid.org/0000-0002-0851-6883 \n2024-05-11\nTo make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'\nMatching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318\n\nFormer definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188" xsd:string {http://purl.org/dc/elements/1.1/contributor="jgiron https://orcid.org/0000-0002-0851-6883", creation_date="2024-02-14"}
[Term]
id: AISM:0000377
@@ -6014,7 +6014,6 @@ def: "An occurrent that has temporal proper parts and for some time t, p s-depen
def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {IAO:0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"}
comment: An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t.
is_a: BFO:0000003 ! occurrent
-relationship: part_of BFO:0000015 {all_only="true"} ! process
property_value: BFO:0000179 "process" xsd:string
property_value: BFO:0000180 "Process" xsd:string
property_value: editor_note "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string
@@ -6096,7 +6095,6 @@ def: "b is a specifically dependent continuant = Def. b is a continuant & there
comment: A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
is_a: BFO:0000002 ! continuant
disjoint_from: BFO:0000031 ! generically dependent continuant
-relationship: has_part BFO:0000020 {all_only="true"} ! characteristic
relationship: part_of BFO:0000020 {all_only="true"} ! characteristic
property_value: BFO:0000179 "sdc" xsd:string
property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string
@@ -29154,7 +29152,6 @@ synonym: "single organism process" RELATED []
synonym: "single-organism process" RELATED []
xref: Wikipedia:Biological_process
is_a: BFO:0000015 ! process
-relationship: has_part GO:0003674 ! molecular_function
property_value: IAO:0000233 "https://github.com/geneontology/go-ontology/issues/24968" xsd:anyURI
created_by: jl
creation_date: 2012-09-19T15:05:24Z
@@ -41513,7 +41510,7 @@ id: GO:0042391
name: regulation of membrane potential
namespace: biological_process
def: "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732]
-is_a: BFO:0000015 ! process
+is_a: BFO:0000003 ! occurrent
relationship: has_part GO:0034220 ! monoatomic ion transmembrane transport
[Term]
@@ -62501,6 +62498,7 @@ id: GO:0100001
name: regulation of skeletal muscle contraction by action potential
namespace: biological_process
def: "Any action potential process that regulates skeletal muscle contraction." [GOC:cjm, GOC:obol]
+is_a: BFO:0000015 ! process
is_a: GO:0001508 ! action potential
intersection_of: GO:0001508 ! action potential
intersection_of: regulates GO:0003009 ! skeletal muscle contraction
@@ -136246,6 +136244,8 @@ synonym: "utilizes" BROAD []
xref: RO:0017001
property_value: curator_notes "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string
property_value: curator_notes "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9625-1899
+property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2620-0345
property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string
property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899
property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345
@@ -136764,7 +136764,6 @@ property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string
property_value: IAO:0000118 "bearer_of" xsd:string
property_value: IAO:0000118 "is bearer of" xsd:string
property_value: RO:0001900 RO:0001901
-property_value: seeAlso "https://github.com/oborel/obo-relations/pull/284" xsd:string
range: BFO:0000020 ! characteristic
is_inverse_functional: true
@@ -137081,7 +137080,6 @@ property_value: IAO:0000112 "this investigation has participant this investigato
property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string
property_value: IAO:0000118 "has_participant" xsd:string
domain: BFO:0000003 ! occurrent
-domain: BFO:0000015 ! process
range: BFO:0000002 ! continuant
holds_over_chain: has_part has_participant
diff --git a/aism-full.owl b/aism-full.owl
index b6bd4ed..0a2d557 100644
--- a/aism-full.owl
+++ b/aism-full.owl
@@ -42,7 +42,7 @@
xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"
xmlns:caloha-reqs-vetted="http://purl.obolibrary.org/obo/caloha-reqs-vetted#">
-
+
http://purl.obolibrary.org/obo/AISM_0000174
http://purl.obolibrary.org/obo/PATO_0000001
http://purl.obolibrary.org/obo/UBERON_0001062
@@ -54,7 +54,7 @@
The ontology for the Anatomy of the Insect SkeletoMuscular system (AISM) contains terms used to describe the cuticle - as a single anatomical structure - and the skeletal muscle system, to be used in insect biodiversity research.
Ontology for the Anatomy of the Insect SkeletoMuscular system
- 2024-03-16
+ 2024-05-11
@@ -3148,9 +3148,7 @@ every c that is a concretization of g specifically denotes r
RO:0000053
has_characteristic
- has characteristic
has characteristic
- https://github.com/oborel/obo-relations/pull/284
@@ -3181,7 +3179,6 @@ every c that is a concretization of g specifically denotes r
-
@@ -3198,7 +3195,6 @@ every c that is a concretization of g specifically denotes r
http://www.obofoundry.org/ro/#OBO_REL:has_participant
RO:0000057
has_participant
- has participant
has participant
@@ -5628,7 +5624,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.RO:0002333
enabled_by
- enabled by
enabled by
https://wiki.geneontology.org/Enabled_by
@@ -7853,6 +7848,8 @@ For example, A and B may be gene products and binding of B by A positively regul
A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input.
See github ticket https://github.com/oborel/obo-relations/issues/497
+
+
2021-11-08T12:00:00Z
2021-11-08T12:00:00Z
utilizes
@@ -25810,15 +25807,20 @@ gmontanaro https://orcid.org/0000-0003-0836-1364
- The anatomical space adjacent to two cuticular punctures.
- Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
+ The distance between two cuticular punctures.
+ Edited by jgiron https://orcid.org/0000-0002-0851-6883
+2024-05-11
+To make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'
+Matching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318
+
+Former definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
interpunctural distance
-
+
-
+
@@ -25833,14 +25835,19 @@ gmontanaro https://orcid.org/0000-0003-0836-1364
- The anatomical space adjacent to two cuticular punctures.
+ The distance between two cuticular punctures.
gmontanaro https://orcid.org/0000-0003-0836-1364
2023-06-04
- Definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
+ Edited by jgiron https://orcid.org/0000-0002-0851-6883
+2024-05-11
+To make it a distance as opposed to an anatomical space and change 'adjacent to' for 'characteristic of'
+Matching existing definitions e.g. http://purl.obolibrary.org/obo/AGRO_00000318
+
+Former definition based on suggestions at https://github.com/obophenotype/uberon/issues/3188
jgiron https://orcid.org/0000-0002-0851-6883
2024-02-14
@@ -53910,12 +53917,6 @@ starasov https://orcid.org/0000-0001-5237-2330
-
-
-
-
-
-
process
Process
a process of cell-division, \ a beating of the heart
@@ -54113,12 +54114,6 @@ starasov https://orcid.org/0000-0001-5237-2330
-
-
-
-
-
-
sdc
SpecificallyDependentContinuant
@@ -98895,21 +98890,21 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion.
https://orcid.org/0000-0002-1425-877X
2023-10-13T11:22:42Z
UB cell
ureteric bud cell
-
+
-
+
PMID:9374839
@@ -114880,7 +114875,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -114905,14 +114900,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0005319
lipid transporter activity
-
+
-
+
GO_REF:0000090
@@ -114993,7 +114988,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -115014,14 +115009,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0005326
neurotransmitter transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -115250,32 +115245,32 @@ The modern definition of neurosecretion has evolved to include the release of an
+
-
A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
Wikipedia:Collagen
cellular_component
GO:0005581
collagen trimer
-
+
-
+
-
+
PMID:12382326
-
+
PMID:12382326
@@ -124820,12 +124815,6 @@ The modern definition of neurosecretion has evolved to include the release of an
-
-
-
-
-
-
A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
A process that emerges from two or more causally-connected macromolecular activities and has evolved to achieve a biological objective.
@@ -125336,7 +125325,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
Enables the transfer of a protein from one side of a membrane to the other.
GO:0015266
GO:0015463
@@ -125365,14 +125354,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0008320
protein transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -136630,7 +136619,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -136645,14 +136634,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015075
monoatomic ion transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -136943,7 +136932,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -136966,14 +136955,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015114
phosphate ion transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -137007,7 +136996,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -137031,14 +137020,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015116
sulfate transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -137083,7 +137072,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -137095,14 +137084,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015123
acetate transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -137277,7 +137266,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -137292,14 +137281,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015144
carbohydrate transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -137371,7 +137360,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -137385,14 +137374,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015149
hexose transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -137477,7 +137466,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -137541,14 +137530,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:0015171
amino acid transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -164542,7 +164531,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -229702,6 +229691,7 @@ The modern definition of neurosecretion has evolved to include the release of an
+
@@ -243635,7 +243625,7 @@ The modern definition of neurosecretion has evolved to include the release of an
-
+
@@ -243650,14 +243640,14 @@ The modern definition of neurosecretion has evolved to include the release of an
GO:1901505
carbohydrate derivative transmembrane transporter activity
-
+
-
+
GO_REF:0000090
@@ -313393,9 +313383,9 @@ When there is no such string, it is almost always because the entities take the
-
-
-
+
+
+
@@ -313439,34 +313429,34 @@ When there is no such string, it is almost always because the entities take the
islet of Langerhans
http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png
-
+
-
+
-
+
-
+
PMID:16417468
-
+
PMID:16417468
-
+
PMID:16417468
@@ -313774,7 +313764,7 @@ When there is no such string, it is almost always because the entities take the
-
+
@@ -313820,7 +313810,7 @@ When there is no such string, it is almost always because the entities take the
sympathetic nervous system
http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png
-
+
@@ -313833,7 +313823,7 @@ When there is no such string, it is almost always because the entities take the
-
+
FMA
MA
ZFA-modified-from-isa
@@ -314039,7 +314029,7 @@ When there is no such string, it is almost always because the entities take the
-
+
@@ -314052,9 +314042,9 @@ When there is no such string, it is almost always because the entities take the
-
-
-
+
+
+
@@ -314102,19 +314092,19 @@ When there is no such string, it is almost always because the entities take the
endocrine pancreas
-
+
-
+
-
+
-
+
@@ -314127,7 +314117,7 @@ When there is no such string, it is almost always because the entities take the
-
+
AAO
FMA
XAO
@@ -314135,19 +314125,19 @@ When there is no such string, it is almost always because the entities take the
-
+
GO
-
+
GO
-
+
GO
@@ -314358,7 +314348,7 @@ When there is no such string, it is almost always because the entities take the
-
+
@@ -314386,14 +314376,14 @@ When there is no such string, it is almost always because the entities take the
compound eye
https://github.com/obophenotype/uberon/issues/457
-
+
-
+
PMID:21062451
@@ -314475,7 +314465,7 @@ When there is no such string, it is almost always because the entities take the
-
+
@@ -314516,14 +314506,14 @@ When there is no such string, it is almost always because the entities take the
camera-type eye
-
+
-
+
definitional
@@ -314961,7 +314951,7 @@ When there is no such string, it is almost always because the entities take the
-
+
A lamina propria that is part of a respiratory airway.
EMAPA:35877
FMA:265157
@@ -314984,14 +314974,14 @@ When there is no such string, it is almost always because the entities take the
UBERON:0000031
lamina propria of trachea
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -315302,8 +315292,8 @@ When there is no such string, it is almost always because the entities take the
-
-
+
+
@@ -315354,11 +315344,11 @@ When there is no such string, it is almost always because the entities take the
tendon
http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg
-
+
-
+
@@ -315371,13 +315361,13 @@ When there is no such string, it is almost always because the entities take the
-
+
OG
-
+
AEO
@@ -315452,8 +315442,8 @@ When there is no such string, it is almost always because the entities take the
-
-
+
+
A biological tissue mass, most commonly a mass of nerve cell bodies.
TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.
@@ -315505,11 +315495,11 @@ When there is no such string, it is almost always because the entities take the
ganglion
-
+
-
+
@@ -315522,13 +315512,13 @@ When there is no such string, it is almost always because the entities take the
-
+
EHDAA2
-
+
Bgee:AN
@@ -315720,7 +315710,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -315780,14 +315770,14 @@ https://doi.org/10.1515/9783110264043
ureter
https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg
-
+
-
+
GO
@@ -315859,8 +315849,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -315910,25 +315900,25 @@ https://doi.org/10.1515/9783110264043
urethra
https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png
-
+
-
+
-
+
pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra
Wikipedia
-
+
Wikipedia
@@ -316471,7 +316461,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -316492,14 +316482,14 @@ https://doi.org/10.1515/9783110264043
respiratory tract
-
+
-
+
NCBIBook:NBK10107
@@ -317162,7 +317152,7 @@ https://doi.org/10.1515/9783110264043
-
+
The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm.
merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)
@@ -317188,7 +317178,7 @@ https://doi.org/10.1515/9783110264043
external ectoderm
http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png
-
+
@@ -317201,7 +317191,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -317625,15 +317615,15 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
-
+
@@ -317669,34 +317659,34 @@ https://doi.org/10.1515/9783110264043
metanephros
-
+
-
+
-
+
-
+
definitional
-
+
GO
-
+
ISBN:9780878932504
@@ -317852,8 +317842,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP].
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]
Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541].
@@ -317880,11 +317870,11 @@ https://doi.org/10.1515/9783110264043
ureteric bud
-
+
-
+
@@ -317897,13 +317887,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
ISBN:9780878932504
@@ -317989,7 +317979,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -318032,14 +318022,14 @@ https://doi.org/10.1515/9783110264043
morula
http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png
-
+
-
+
EHDAA2
@@ -318196,8 +318186,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
A mass of cells that develop into the body of the embryo and some extraembryonic tissues.
A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]
A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]
@@ -318225,24 +318215,24 @@ https://doi.org/10.1515/9783110264043
inner cell mass
https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg
-
+
-
+
-
+
Wikipedia
-
+
Wikipedia
@@ -318309,7 +318299,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -318342,14 +318332,14 @@ https://doi.org/10.1515/9783110264043
trophoblast
https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg
-
+
-
+
MP-def
PMID:19829370
@@ -318415,7 +318405,7 @@ https://doi.org/10.1515/9783110264043
-
+
A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc.
embryonic disc
embryonic shield
@@ -318435,14 +318425,14 @@ https://doi.org/10.1515/9783110264043
bilaminar disc
http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png
-
+
-
+
Wikipedia
@@ -318543,7 +318533,7 @@ https://doi.org/10.1515/9783110264043
-
+
Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA].
2009-07-30T05:19:13Z
@@ -318554,14 +318544,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0000094
membrane organ
-
+
-
+
FMA-def
@@ -318584,7 +318574,7 @@ https://doi.org/10.1515/9783110264043
-
+
Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia].
A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751].
ZFA treats this as a subtype of NC.
@@ -318601,14 +318591,14 @@ https://doi.org/10.1515/9783110264043
cardiac neural crest
-
+
-
+
Wikipedia
@@ -319075,7 +319065,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -319111,14 +319101,14 @@ https://doi.org/10.1515/9783110264043
gastrula stage
-
+
-
+
BILS
@@ -319637,7 +319627,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -319665,7 +319655,7 @@ https://doi.org/10.1515/9783110264043
lung bud
http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png
-
+
@@ -319678,7 +319668,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -319790,7 +319780,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -319816,14 +319806,14 @@ https://doi.org/10.1515/9783110264043
neural nucleus
-
+
-
+
we limit this structure by definition to chordate and vertebrate nervous systems
@@ -320040,7 +320030,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -320079,14 +320069,14 @@ https://doi.org/10.1515/9783110264043
anal canal
https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png
-
+
-
+
Wikipathways:WP2062
@@ -320269,8 +320259,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -320303,24 +320293,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0000162
cloaca
-
+
-
+
-
+
ZFA
-
+
AAO
@@ -320402,8 +320392,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -320422,24 +320412,24 @@ https://doi.org/10.1515/9783110264043
embryonic cloaca
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -320462,7 +320452,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -320504,14 +320494,14 @@ https://doi.org/10.1515/9783110264043
primitive urogenital sinus
http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png
-
+
-
+
MP-def
@@ -321067,7 +321057,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -321113,14 +321103,14 @@ https://doi.org/10.1515/9783110264043
pair of lungs
-
+
-
+
FMA-abduced
@@ -321295,21 +321285,21 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
-
+
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
@@ -321353,34 +321343,34 @@ https://doi.org/10.1515/9783110264043
blood
-
+
-
+
-
+
-
+
CL:tm
-
+
https://github.com/obophenotype/uberon/issues/1330
-
+
Bgee:AN
@@ -321496,7 +321486,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -321531,7 +321521,7 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png
https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png
-
+
@@ -321544,7 +321534,7 @@ https://doi.org/10.1515/9783110264043
-
+
cjm
@@ -321747,7 +321737,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -321780,14 +321770,14 @@ https://doi.org/10.1515/9783110264043
atlanto-occipital joint
http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png
-
+
-
+
FMA-abduced-lr
@@ -322243,7 +322233,7 @@ https://doi.org/10.1515/9783110264043
-
+
The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin.
BTO:0000503
EMAPA:27181
@@ -322254,7 +322244,7 @@ https://doi.org/10.1515/9783110264043
gastric gland
-
+
@@ -322267,7 +322257,7 @@ https://doi.org/10.1515/9783110264043
-
+
ISBN:0073040584
@@ -323219,7 +323209,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -323246,7 +323236,7 @@ https://doi.org/10.1515/9783110264043
syncytiotrophoblast
http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png
-
+
@@ -323259,7 +323249,7 @@ https://doi.org/10.1515/9783110264043
-
+
EMAPA
@@ -324622,7 +324612,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -324664,14 +324654,14 @@ https://doi.org/10.1515/9783110264043
organism substance
-
+
-
+
this relationship may be too strong and may be weakened in future
@@ -325922,7 +325912,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -325966,14 +325956,14 @@ https://doi.org/10.1515/9783110264043
epithelium
https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg
-
+
-
+
http://palaeos.com/metazoa/porifera/homoscleromorpha.html
@@ -326574,7 +326564,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -326611,14 +326601,14 @@ https://doi.org/10.1515/9783110264043
abdomen
-
+
-
+
MA
@@ -326881,7 +326871,7 @@ https://doi.org/10.1515/9783110264043
-
+
Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue.
Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
@@ -326919,14 +326909,14 @@ https://doi.org/10.1515/9783110264043
ectoderm
http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png
-
+
-
+
Bgee:AN
@@ -326991,7 +326981,7 @@ https://doi.org/10.1515/9783110264043
-
+
Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut.
The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]
endodermal
@@ -327028,14 +327018,14 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png
http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png
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Bgee:AN
@@ -327102,7 +327092,7 @@ https://doi.org/10.1515/9783110264043
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mesoderm
http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png
-
+
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Bgee:AN
@@ -327377,7 +327367,7 @@ https://doi.org/10.1515/9783110264043
-
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proctodeum
https://github.com/obophenotype/uberon/issues/685
-
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-
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EHDAA2
@@ -327513,7 +327503,7 @@ https://doi.org/10.1515/9783110264043
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-
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stomach
https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg
-
+
-
+
@@ -327657,14 +327647,14 @@ https://doi.org/10.1515/9783110264043
-
+
absent in lampreys and hagfishes
ISBN:0073040584
-
+
ISBN:0486692132
@@ -327758,7 +327748,7 @@ https://doi.org/10.1515/9783110264043
-
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@@ -327807,7 +327797,7 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg
-
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@@ -327820,7 +327810,7 @@ https://doi.org/10.1515/9783110264043
-
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EHDAA2
@@ -327900,7 +327890,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -328009,14 +327999,14 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb
-
+
-
+
MA
@@ -328212,7 +328202,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -328243,7 +328233,7 @@ https://doi.org/10.1515/9783110264043
-
+
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
@@ -328307,11 +328297,11 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb
-
+
-
+
@@ -328324,13 +328314,13 @@ https://doi.org/10.1515/9783110264043
-
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FMA
-
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Bgee:AN
@@ -328583,9 +328573,9 @@ https://doi.org/10.1515/9783110264043
-
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cornea
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
-
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-
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-
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MA
-
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MA
-
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FMA-isa
-
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definitional
@@ -328893,9 +328883,9 @@ https://doi.org/10.1515/9783110264043
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+
@@ -328906,7 +328896,7 @@ https://doi.org/10.1515/9783110264043
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retina
http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png
-
+
-
+
-
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-
+
-
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FMA
-
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FMA
-
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FMA
-
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EHDAA2
@@ -329074,8 +329064,8 @@ https://doi.org/10.1515/9783110264043
-
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@@ -329111,24 +329101,24 @@ https://doi.org/10.1515/9783110264043
eye
-
+
-
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-
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PMID:21062451
-
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PMID:21062451
@@ -329305,7 +329295,7 @@ https://doi.org/10.1515/9783110264043
-
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@@ -329319,7 +329309,7 @@ https://doi.org/10.1515/9783110264043
-
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pleura
http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png
-
+
-
+
https://github.com/obophenotype/uberon/issues/86
@@ -329568,7 +329558,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -329637,14 +329627,14 @@ https://doi.org/10.1515/9783110264043
pons
http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png
-
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-
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neuronames
@@ -329713,8 +329703,8 @@ https://doi.org/10.1515/9783110264043
-
-
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+
An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination.
penile
phallic
@@ -329750,11 +329740,11 @@ https://doi.org/10.1515/9783110264043
penis
http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg
-
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-
+
@@ -329767,13 +329757,13 @@ https://doi.org/10.1515/9783110264043
-
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Wikipedia
-
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EHDAA2
@@ -331084,7 +331074,7 @@ https://doi.org/10.1515/9783110264043
-
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@@ -331154,14 +331144,14 @@ https://doi.org/10.1515/9783110264043
vas deferens
http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg
-
+
-
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FMA
@@ -331293,7 +331283,7 @@ https://doi.org/10.1515/9783110264043
-
+
Tough but flexible, non-mineral outer coverings of an organism, or parts of an organism, that provide protection. Cuticles are non-homologous, differing in their origin, structure and chemical composition[WP].
cuticular
BTO:0001600
@@ -331308,14 +331298,14 @@ https://doi.org/10.1515/9783110264043
EDITOR_NOTE TODO - check cuticle vs exoskeleton. Note that GO has a very generic definition of cuticle. See also arthropod-anatomy ontology. Note in ncit Cuticle is a plant part
cuticle
-
+
-
+
Rieger - Evolution of the Cuticle in the Lower Eumetazoa
@@ -332454,7 +332444,7 @@ https://doi.org/10.1515/9783110264043
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http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg
http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png
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Bgee:AN
@@ -332638,7 +332628,7 @@ https://doi.org/10.1515/9783110264043
-
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@@ -332693,7 +332683,7 @@ https://doi.org/10.1515/9783110264043
central nervous system
-
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Bgee:AN
@@ -332934,7 +332924,7 @@ https://doi.org/10.1515/9783110264043
-
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A nerve that transmits from sensory receptors on the surface of the body to the central nervous system.
AEO:0000201
EHDAA2:0003200
@@ -332949,14 +332939,14 @@ https://doi.org/10.1515/9783110264043
sensory nerve
-
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AEO
@@ -333112,8 +333102,8 @@ https://doi.org/10.1515/9783110264043
-
-
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+
A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP].
consider splitting class
One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]
@@ -333144,11 +333134,11 @@ https://doi.org/10.1515/9783110264043
yolk sac
http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png
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ISBN:0073040584
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ISBN:0073040584
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-
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A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED].
A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867].
Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]
@@ -333374,14 +333364,14 @@ https://doi.org/10.1515/9783110264043
Consider generalizing to deuterostome pharynx
chordate pharynx
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EHDAA2
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hindgut
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png
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Wikipedia
@@ -334000,15 +333990,15 @@ https://doi.org/10.1515/9783110264043
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https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb
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MA
-
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EHDAA2
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ISBN:0073040584
@@ -334196,7 +334186,7 @@ https://doi.org/10.1515/9783110264043
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ventral pancreatic duct
http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png
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EHDAA2
@@ -334341,7 +334331,7 @@ https://doi.org/10.1515/9783110264043
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A zone of skin that is part of a back [Automatically generated definition].
EMAPA:36392
FMA:10462
@@ -334358,7 +334348,7 @@ https://doi.org/10.1515/9783110264043
EDITOR_NOTE TODO - distinguish between entire skin of region and arbitrary zone of skin on region
skin of back
-
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MA
@@ -334405,9 +334395,9 @@ https://doi.org/10.1515/9783110264043
-
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A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP].
not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO
@@ -334440,15 +334430,15 @@ https://doi.org/10.1515/9783110264043
https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722
http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif
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FMA
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EHDAA2
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FMA
@@ -334790,14 +334780,14 @@ https://doi.org/10.1515/9783110264043
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pericardial cavity
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FMA
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Wikipedia
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endocardium of ventricle
-
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https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -335111,7 +335101,7 @@ https://doi.org/10.1515/9783110264043
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@@ -335139,14 +335129,14 @@ https://doi.org/10.1515/9783110264043
myocardium of ventricle
-
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https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -335657,7 +335647,7 @@ https://doi.org/10.1515/9783110264043
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The second vertebral bone in the vertebral column.
Vertebra that is posteriorly adjacent to vertebra 1.[TAO]
@@ -335693,14 +335683,14 @@ https://doi.org/10.1515/9783110264043
vertebral bone 2
-
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FMA
@@ -336001,7 +335991,7 @@ https://doi.org/10.1515/9783110264043
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diaphragm
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PMID:23586979
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definitional
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vertebral column
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cjm
@@ -337155,7 +337145,7 @@ https://doi.org/10.1515/9783110264043
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Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri).
AEO:0000111
BTO:0002422
@@ -337180,14 +337170,14 @@ https://doi.org/10.1515/9783110264043
mesothelium
http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg
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FMA
@@ -337302,7 +337292,7 @@ https://doi.org/10.1515/9783110264043
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In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
BTO:0002783
@@ -337325,14 +337315,14 @@ https://doi.org/10.1515/9783110264043
superior mesenteric vein
http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png
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Wikipedia:Vitelline_vein
@@ -337374,7 +337364,7 @@ https://doi.org/10.1515/9783110264043
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A vein that drains the pelvis and lower limbs into the inferior vena cava.
In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries.
@@ -337397,7 +337387,7 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif
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FMA-abduced-lr
@@ -337719,7 +337709,7 @@ https://doi.org/10.1515/9783110264043
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Vein that carries blood away from the liver[ZFA].
todo - add developmental relationships for other taxa
@@ -337750,14 +337740,14 @@ https://doi.org/10.1515/9783110264043
hepatic vein
http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png
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FMA-abduced-lr
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http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg
http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png
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EHDAA2
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colon
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FMA
@@ -338372,7 +338362,7 @@ https://doi.org/10.1515/9783110264043
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The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
BTO:0000645
@@ -338404,7 +338394,7 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb
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Wikipedia
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pyloric antrum
http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg
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Wikipedia
@@ -339093,7 +339083,7 @@ https://doi.org/10.1515/9783110264043
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portal lobule
-
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MA
MP
@@ -339147,7 +339137,7 @@ https://doi.org/10.1515/9783110264043
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UBERON:0001172
hepatic acinus
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cjm
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common hepatic duct
http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg
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Wikipedia
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Wikipedia
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definitional
@@ -339760,7 +339750,7 @@ https://doi.org/10.1515/9783110264043
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peritoneal cavity
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Wikipedia
@@ -341932,8 +341922,8 @@ https://doi.org/10.1515/9783110264043
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A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP].
currently defined as equivalent to any submucosal gland in the duodenum.
Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds
@@ -341959,11 +341949,11 @@ https://doi.org/10.1515/9783110264043
duodenal gland
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@@ -341976,13 +341966,13 @@ https://doi.org/10.1515/9783110264043
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FMA, modified
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unclear for Aves
ISBN:9780521617147
@@ -342038,7 +342028,7 @@ https://doi.org/10.1515/9783110264043
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intestinal villus
http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg
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ZFA
@@ -342210,7 +342200,7 @@ https://doi.org/10.1515/9783110264043
-
+
A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted].
BTO:0002782
@@ -342234,14 +342224,14 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
-
+
-
+
FMA/obol
@@ -342389,14 +342379,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
@@ -342448,24 +342438,24 @@ https://doi.org/10.1515/9783110264043
renal pelvis
https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg
-
+
-
+
-
+
MA
-
+
FMA
@@ -342511,7 +342501,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -342548,14 +342538,14 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb
https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg
-
+
-
+
FMA
@@ -342584,11 +342574,11 @@ https://doi.org/10.1515/9783110264043
-
+
-
-
+
+
@@ -342627,7 +342617,7 @@ https://doi.org/10.1515/9783110264043
nephron tubule
-
+
@@ -342636,18 +342626,18 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
-
+
GO
MA
ZFA
@@ -342661,13 +342651,13 @@ https://doi.org/10.1515/9783110264043
-
+
ZFA
-
+
checkme
@@ -342708,7 +342698,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -342756,14 +342746,14 @@ https://doi.org/10.1515/9783110264043
collecting duct of renal tubule
-
+
-
+
checkme
GO
@@ -343493,7 +343483,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -343525,7 +343515,7 @@ https://doi.org/10.1515/9783110264043
interlobular bile duct
-
+
@@ -343539,7 +343529,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
MA
MP
@@ -343581,7 +343571,7 @@ https://doi.org/10.1515/9783110264043
-
+
An adventitia that is part of a ureter.
EMAPA:28114
FMA:15892
@@ -343597,14 +343587,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0001252
adventitia of ureter
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -343648,7 +343638,7 @@ https://doi.org/10.1515/9783110264043
-
+
A lamina propria that is part of a ureter [Automatically generated definition].
EMAPA:28841
@@ -343665,14 +343655,14 @@ https://doi.org/10.1515/9783110264043
lamina propria of ureter
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -343715,7 +343705,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -343726,7 +343716,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -343779,11 +343769,11 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb
https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg
-
+
-
+
@@ -343796,13 +343786,13 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
-
+
upper part of UG sinus
@@ -344110,7 +344100,7 @@ https://doi.org/10.1515/9783110264043
-
+
A serous membrane that is part of a urinary bladder [Automatically generated definition].
TODO - check serosa/peritoneum
EMAPA:28661
@@ -344133,14 +344123,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0001260
serosa of urinary bladder
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -344429,7 +344419,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -344461,14 +344451,14 @@ https://doi.org/10.1515/9783110264043
pancreatic acinus
-
+
-
+
FMA
@@ -344517,9 +344507,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO].
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
@@ -344565,34 +344555,34 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb
https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png
-
+
-
+
-
+
-
+
PMID:16417468
-
+
Wikipedia
-
+
Wikipedia
@@ -344657,7 +344647,7 @@ https://doi.org/10.1515/9783110264043
-
+
A trabecula that is part of a spleen.
EMAPA:35808
@@ -344675,14 +344665,14 @@ https://doi.org/10.1515/9783110264043
trabecula of spleen
-
+
-
+
FMA
@@ -345267,7 +345257,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -345297,14 +345287,14 @@ https://doi.org/10.1515/9783110264043
liver parenchyma
-
+
-
+
XAO
@@ -345379,7 +345369,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -345429,14 +345419,14 @@ https://doi.org/10.1515/9783110264043
hepatic sinusoid
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -345501,8 +345491,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -345545,11 +345535,11 @@ https://doi.org/10.1515/9783110264043
intralobular bile duct
-
+
-
+
@@ -345562,13 +345552,13 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
-
+
FMA
@@ -345630,7 +345620,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -345643,7 +345633,7 @@ https://doi.org/10.1515/9783110264043
-
+
The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP].
kidney terms require review for cross-vertebrate compatibility and developmental relationships.
@@ -345676,24 +345666,24 @@ https://doi.org/10.1515/9783110264043
nephron
http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png
-
+
-
+
-
+
FMA
-
+
Bgee:AN
@@ -345762,7 +345752,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -345812,14 +345802,14 @@ https://doi.org/10.1515/9783110264043
endometrium
https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg
-
+
-
+
FMA
@@ -345906,7 +345896,7 @@ https://doi.org/10.1515/9783110264043
-
+
Outer serosa layer of the uterus.
TODO - check for parallel structure with peritoneum
EMAPA:37792
@@ -345930,14 +345920,14 @@ https://doi.org/10.1515/9783110264043
serosa of uterus
https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -346026,7 +346016,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -346056,14 +346046,14 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg
https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png
-
+
-
+
Bgee:AN
@@ -346107,14 +346097,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
@@ -346169,24 +346159,24 @@ https://doi.org/10.1515/9783110264043
epididymis
http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg
-
+
-
+
-
+
FMA
-
+
Wikipedia
@@ -346559,7 +346549,7 @@ https://doi.org/10.1515/9783110264043
-
+
Muscle (organ) which is a part of the pelvis. Examples: levator ani,.
@@ -346577,7 +346567,7 @@ https://doi.org/10.1515/9783110264043
muscle of pelvis
-
+
@@ -346589,7 +346579,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMAdef
@@ -346985,7 +346975,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -347030,14 +347020,14 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg
http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png
-
+
-
+
Wikipedia
@@ -347116,7 +347106,7 @@ https://doi.org/10.1515/9783110264043
-
+
The anus and surrounding regions. Encompasses both internal and external regions, where present.
Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]
EFO:0000847
@@ -347142,14 +347132,14 @@ https://doi.org/10.1515/9783110264043
https://github.com/obophenotype/uberon/issues/507
http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png
-
+
-
+
cjm
@@ -348013,7 +348003,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -348024,7 +348014,7 @@ https://doi.org/10.1515/9783110264043
-
+
Skeletal element that is composed of bone tissue.
@@ -348074,14 +348064,14 @@ https://doi.org/10.1515/9783110264043
bone element
-
+
-
+
VSAO-modified
@@ -348279,7 +348269,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -348323,14 +348313,14 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
-
+
-
+
EHDAA2
@@ -348385,7 +348375,7 @@ https://doi.org/10.1515/9783110264043
-
+
Any muscle organ that is part of a pelvic girdle [Automatically generated definition].
Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle.
UBERON:0003271
@@ -348407,14 +348397,14 @@ https://doi.org/10.1515/9783110264043
muscle of pelvic girdle
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -348484,7 +348474,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -348532,14 +348522,14 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
-
+
-
+
left arch 4 in human
embryology.ch
@@ -348603,7 +348593,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -348639,7 +348629,7 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
-
+
@@ -348652,7 +348642,7 @@ https://doi.org/10.1515/9783110264043
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Wikipedia
@@ -348791,7 +348781,7 @@ https://doi.org/10.1515/9783110264043
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@@ -348840,14 +348830,14 @@ https://doi.org/10.1515/9783110264043
abdominal aorta
http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png
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-
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FMA
@@ -349029,7 +349019,7 @@ https://doi.org/10.1515/9783110264043
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@@ -349067,7 +349057,7 @@ https://doi.org/10.1515/9783110264043
common carotid artery plus branches
http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg
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@@ -349080,7 +349070,7 @@ https://doi.org/10.1515/9783110264043
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Wikipedia
@@ -349158,8 +349148,8 @@ https://doi.org/10.1515/9783110264043
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+
One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta.
Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)
@@ -349197,24 +349187,24 @@ https://doi.org/10.1515/9783110264043
subclavian artery
http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg
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-
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EHDAA2
-
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EHDAA2
@@ -349403,7 +349393,7 @@ https://doi.org/10.1515/9783110264043
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@@ -349458,14 +349448,14 @@ https://doi.org/10.1515/9783110264043
digestive tract
-
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-
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NCBIBook:NBK10107
@@ -349989,7 +349979,7 @@ https://doi.org/10.1515/9783110264043
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+
The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted].
BTO:0000654
@@ -350012,7 +350002,7 @@ https://doi.org/10.1515/9783110264043
ciliary muscle
http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png
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+
@@ -350031,7 +350021,7 @@ https://doi.org/10.1515/9783110264043
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FMA
@@ -350155,10 +350145,10 @@ https://doi.org/10.1515/9783110264043
-
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A sphincter muscle that is part of the iris.
In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]
WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure
@@ -350193,19 +350183,19 @@ https://doi.org/10.1515/9783110264043
sphincter pupillae
http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png
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@@ -350218,27 +350208,27 @@ https://doi.org/10.1515/9783110264043
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ISBN:0781772214
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encircles iris
dbpedia
-
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encircles iris
dbpedia
-
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dbpedia
@@ -350351,10 +350341,10 @@ https://doi.org/10.1515/9783110264043
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A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted].
It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina
@@ -350391,19 +350381,19 @@ https://doi.org/10.1515/9783110264043
dilatator pupillae
http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png
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@@ -350416,27 +350406,27 @@ https://doi.org/10.1515/9783110264043
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ISBN:0781772214
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outer margins of iris
dbpedia
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inner margins of iris
dbpedia
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dbpedia
@@ -351130,10 +351120,10 @@ https://doi.org/10.1515/9783110264043
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The first major branch of the abdominal aorta.
EHDAA2:0004519
@@ -351165,44 +351155,44 @@ https://doi.org/10.1515/9783110264043
celiac artery
http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png
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ISBN:0073040584
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ISBN:0073040584
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ISBN:0073040584
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ISBN:0073040584
@@ -351323,7 +351313,7 @@ https://doi.org/10.1515/9783110264043
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@@ -351385,14 +351375,14 @@ https://doi.org/10.1515/9783110264043
trigeminal nerve
https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png
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Wikipedia
@@ -351677,7 +351667,7 @@ https://doi.org/10.1515/9783110264043
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The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted].
Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]
@@ -351701,14 +351691,14 @@ https://doi.org/10.1515/9783110264043
facial vein
http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png
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FMA
@@ -351790,7 +351780,7 @@ https://doi.org/10.1515/9783110264043
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@@ -351851,7 +351841,7 @@ https://doi.org/10.1515/9783110264043
trigeminal ganglion
http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png
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@@ -351864,7 +351854,7 @@ https://doi.org/10.1515/9783110264043
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Bgee:AN
@@ -351988,11 +351978,11 @@ https://doi.org/10.1515/9783110264043
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+
@@ -352023,23 +352013,23 @@ https://doi.org/10.1515/9783110264043
occipital bone
http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png
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@@ -352052,32 +352042,32 @@ https://doi.org/10.1515/9783110264043
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FMA
-
+
basi paired exo and supra occipital bones
MA-modified
-
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interparietal (postparietal)
-
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WP
-
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PMID:11523816
@@ -352139,10 +352129,10 @@ https://doi.org/10.1515/9783110264043
-
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An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended.
part of viscerocranium (facial skeleton) in FMA
@@ -352171,19 +352161,19 @@ https://doi.org/10.1515/9783110264043
sphenoid bone
http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg
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@@ -352196,25 +352186,25 @@ https://doi.org/10.1515/9783110264043
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orbito pre and basi sphenoid
-
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pterygoid process
-
+
alisphenoid
-
+
cjm
@@ -352283,7 +352273,7 @@ https://doi.org/10.1515/9783110264043
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@@ -352319,7 +352309,7 @@ https://doi.org/10.1515/9783110264043
ethmoid bone
http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg
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@@ -352332,7 +352322,7 @@ https://doi.org/10.1515/9783110264043
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definitional
@@ -352415,7 +352405,7 @@ https://doi.org/10.1515/9783110264043
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@@ -352448,14 +352438,14 @@ https://doi.org/10.1515/9783110264043
orbit of skull
-
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FMA-abduced-lr
@@ -352632,7 +352622,7 @@ https://doi.org/10.1515/9783110264043
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@@ -352698,14 +352688,14 @@ https://doi.org/10.1515/9783110264043
jaw skeleton
-
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cjm
@@ -352915,7 +352905,7 @@ https://doi.org/10.1515/9783110264043
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@@ -352950,14 +352940,14 @@ https://doi.org/10.1515/9783110264043
lower jaw region
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png
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Wikipedia:Mandibular_prominence
@@ -353145,7 +353135,7 @@ https://doi.org/10.1515/9783110264043
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@@ -353170,14 +353160,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0001731
cavity of pharynx
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XAO
@@ -353456,7 +353446,7 @@ https://doi.org/10.1515/9783110264043
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@@ -353499,14 +353489,14 @@ https://doi.org/10.1515/9783110264043
iris
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XAO
@@ -353585,7 +353575,7 @@ https://doi.org/10.1515/9783110264043
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corneal epithelium
http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png
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ISBN:0781772214
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sclera
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
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FMA
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ZFA
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ISBN:0781772214
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-
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A skeletal muscle organ that is part of the trunk region.
Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'.
Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here.
@@ -353894,14 +353884,14 @@ https://doi.org/10.1515/9783110264043
skeletal muscle of trunk
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prolog
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@@ -354011,14 +354001,14 @@ https://doi.org/10.1515/9783110264043
ciliary body
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
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ISBN:0781772214
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optic choroid
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
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MA
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Wikipedia
@@ -354254,7 +354244,7 @@ https://doi.org/10.1515/9783110264043
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substantia propria of cornea
http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png
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-
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cjm
ISBN:0781772214
Wikipedia
@@ -354378,15 +354368,15 @@ https://doi.org/10.1515/9783110264043
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A double layer covering the ciliary body that produces aqueous humor.
BTO:0001770
@@ -354406,15 +354396,15 @@ https://doi.org/10.1515/9783110264043
ciliary epithelium
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MA
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MP
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Wikipedia
@@ -354874,7 +354864,7 @@ https://doi.org/10.1515/9783110264043
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@@ -354910,14 +354900,14 @@ https://doi.org/10.1515/9783110264043
aqueous humor of eyeball
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
-
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FMA def states A and P
located_in in EHDAA2
VHOG
@@ -355047,8 +355037,8 @@ https://doi.org/10.1515/9783110264043
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@@ -355081,24 +355071,24 @@ https://doi.org/10.1515/9783110264043
anterior segment of eyeball
http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png
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FMA
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cjm
@@ -355150,8 +355140,8 @@ https://doi.org/10.1515/9783110264043
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posterior segment of eyeball
http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg
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FMA
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cjm
@@ -355386,7 +355376,7 @@ https://doi.org/10.1515/9783110264043
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The elastic, clear, membrane-like structure, that is outer most layer of the lens.
The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]
@@ -355412,14 +355402,14 @@ https://doi.org/10.1515/9783110264043
capsule of lens
http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png
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EHDAA2
@@ -355595,7 +355585,7 @@ https://doi.org/10.1515/9783110264043
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sympathetic ganglion
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
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DOI:10.1101/gr.157586.113
ISBN:0073040584
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http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG
http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg
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BTO
FMA-implicit
VHOG
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cjm
@@ -356169,14 +356159,14 @@ https://doi.org/10.1515/9783110264043
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The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO].
developmental relationships need revised
@@ -356229,24 +356219,24 @@ https://doi.org/10.1515/9783110264043
midbrain
http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG
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definitional
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Bgee:AN
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Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified].
Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965].
@@ -356503,14 +356493,14 @@ https://doi.org/10.1515/9783110264043
metencephalon
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
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definitional
@@ -356772,7 +356762,7 @@ https://doi.org/10.1515/9783110264043
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An epithelium that is part of a small intestine [Automatically generated definition].
Intestinal epithelium which lines the lumen of the mid intestine.[TAO]
BTO:0001258
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epithelium of small intestine
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FMA
@@ -357202,7 +357192,7 @@ https://doi.org/10.1515/9783110264043
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Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP].
Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]
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midbrain tegmentum
http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png
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ZFA
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bile
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0.3% in humans
@@ -357839,7 +357829,7 @@ https://doi.org/10.1515/9783110264043
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A lamina propria that is part of a esophagus [Automatically generated definition].
EMAPA:26987
FMA:63050
@@ -357868,14 +357858,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0001974
lamina propria of esophagus
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FMA
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epithelium of esophagus
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FMA
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blood vessel
http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg
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AEO
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EHDAA2
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GO:0072360
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Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell.
Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]
@@ -358976,44 +358966,44 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb
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https://github.com/obophenotype/uberon/issues/1376
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ISBN:0073040584
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Wikipedia
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ISBN:0073040584
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An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood..
@@ -359282,35 +359272,35 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png
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Wikipedia
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EHDAA2
XAO
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EHDAA2
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The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA].
@@ -359879,25 +359869,25 @@ https://doi.org/10.1515/9783110264043
hindbrain
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
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modified-source-relation
ABA
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Bgee:AN
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The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted].
@@ -360299,14 +360289,14 @@ https://doi.org/10.1515/9783110264043
pontine raphe nucleus
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Wikipedia
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https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb
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some species only have a single lung
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The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles.
assume spelling error for ncit
EHDAA2:0004143
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truncus arteriosus
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EHDAA2
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EHDAA2
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The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA].
Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]
relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]
@@ -360941,14 +360931,14 @@ https://doi.org/10.1515/9783110264043
endocardial cushion
http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png
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ZFA
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The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart.
Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]
Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]
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sinus venosus
http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png
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VHOG
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Bgee:AN
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The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP].
Consider adding a layer-of-skin grouping class for all skin layers
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dermis
http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg
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definitional
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Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP].
A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]
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hypodermis
http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg
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ZFA
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FMA-modified
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A cardiac ventricle that is in the right side of the heart.
The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]
@@ -361901,24 +361891,24 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb
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PMID:17276708
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cjm
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Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
One of four heart chambers.[TAO]
@@ -362148,14 +362138,14 @@ https://doi.org/10.1515/9783110264043
cardiac ventricle
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Bgee:AN
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A cardiac ventricle that is in the left side of the heart.
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
@@ -362270,14 +362260,14 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb
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GO
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https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb
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Wikipathways:WP2062
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https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb
https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg
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multiple sources - true spleen appear in jawed vertebrates
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https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb
https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg
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ZFA
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ZFA-weakened
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EHDAA2
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http://www.stembook.org/node/512
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https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg
https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg
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definitional
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kidney
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FMA
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definitional
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Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104
pronephros
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ZFA
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superior olivary complex
http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png
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NIFSTD
@@ -364960,7 +364950,7 @@ https://doi.org/10.1515/9783110264043
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locus ceruleus
http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png
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check ZFA
NIFSTD
@@ -365159,7 +365149,7 @@ https://doi.org/10.1515/9783110264043
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Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703).
@@ -365195,14 +365185,14 @@ https://doi.org/10.1515/9783110264043
superior salivatory nucleus
http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png
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definitional
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The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO].
Layer that lines the lumen of the heart.[TAO]
Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]
@@ -365379,14 +365369,14 @@ https://doi.org/10.1515/9783110264043
endocardium
http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png
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Bgee:AN
@@ -365867,7 +365857,7 @@ https://doi.org/10.1515/9783110264043
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integument
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FMA
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Vasculature that is part of the eye region.
not part of the eye in ZFA. Note this changed to a blood vessel in ZFA
@@ -366230,14 +366220,14 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb
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ISBN:0781772214
@@ -366296,7 +366286,7 @@ https://doi.org/10.1515/9783110264043
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musculoskeletal system
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check ctenophore
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Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO).
TODO - add superclass to unify with VNC?
@@ -366707,34 +366697,34 @@ https://doi.org/10.1515/9783110264043
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb
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ZFA
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definitional
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definitional
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ventral horn of spinal cord
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FMA-abduced-lr
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dorsal mesentery
http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png
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EHDAA2
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EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct
coelemic cavity lumen
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definitional
@@ -367953,7 +367943,7 @@ https://doi.org/10.1515/9783110264043
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Any muscle organ that is part of a back [Automatically generated definition].
EMAPA:35161
@@ -367967,14 +367957,14 @@ https://doi.org/10.1515/9783110264043
muscle of back
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prolog
@@ -368190,9 +368180,9 @@ https://doi.org/10.1515/9783110264043
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notochord
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
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@@ -368276,19 +368266,19 @@ https://doi.org/10.1515/9783110264043
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http://tolweb.org/Chordata/2499
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ZFA
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EHDAA2
@@ -368373,7 +368363,7 @@ https://doi.org/10.1515/9783110264043
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@@ -368384,7 +368374,7 @@ https://doi.org/10.1515/9783110264043
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somite
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
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@@ -368453,13 +368443,13 @@ https://doi.org/10.1515/9783110264043
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GOTAX:0000352
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ZFA
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A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP].
EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams).
@@ -368949,66 +368939,66 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png
https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png
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XAO
https://github.com/obophenotype/uberon/wiki/The-neural-crest
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Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells
ISBN:0073040584
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BTO
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PMID:11523831
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pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest
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PMID:11523831
@@ -369381,15 +369371,15 @@ https://doi.org/10.1515/9783110264043
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A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart.
External layer of the heart.[TAO]
@@ -369419,34 +369409,34 @@ https://doi.org/10.1515/9783110264043
EDITOR_NOTE TODO - check links with UBERON:0002425 visceral serous pericardium. develops from proepicardium. WP:Epicardium -- When considered as a part of the pericardium, it is the inner layer, or visceral pericardium, continuous with the serous layer.
epicardium
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multiple
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FMA-inferred
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FMA
@@ -369633,11 +369623,11 @@ https://doi.org/10.1515/9783110264043
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conducting system of heart
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@@ -369703,31 +369693,31 @@ https://doi.org/10.1515/9783110264043
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FMA
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FMA
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FMA
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FMA
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FMA
@@ -369794,7 +369784,7 @@ https://doi.org/10.1515/9783110264043
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@@ -369858,7 +369848,7 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg
http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg
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ZFA
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cardiac Purkinje fiber
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png
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@@ -370202,7 +370192,7 @@ https://doi.org/10.1515/9783110264043
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https://github.com/obophenotype/uberon/issues/1785
https://orcid.org/0000-0001-5208-3432
https://orcid.org/0000-0002-9791-0064
@@ -370210,7 +370200,7 @@ https://doi.org/10.1515/9783110264043
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FMA
@@ -370357,7 +370347,7 @@ https://doi.org/10.1515/9783110264043
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Serous membrane which is divided into parietal and visceral serous pericardium.
EMAPA:19030
FMA:9582
@@ -370384,24 +370374,24 @@ https://doi.org/10.1515/9783110264043
serous pericardium
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FMA
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FMA
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peritoneum
http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png
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MP
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Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA].
most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]
EMAPA:19029
@@ -370563,11 +370553,11 @@ https://doi.org/10.1515/9783110264043
fibrous pericardium
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FMA
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WP
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bone marrow
http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg
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FMA
MA
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defined generically so could in theory encompass FBbt:00003260 'skeletal muscle of head', or the muscle of a starfish Aristotle's lantern, but we restrict this to craniates. Skeletal muscles of the head originate from the non-segmented head mesoderm (Noden, 1983; Wachtler et al., 1984)
cranial muscle
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https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
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EHDAA2-abduced
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Any muscle that is part of the cervical (neck) region.
EMAPA:36050
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muscle of neck
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prolog
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muscle of abdomen
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prolog
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hematopoietic system
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FMA
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definitional
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bile duct
http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png
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EMAPA
MA
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XAO
@@ -371971,7 +371961,7 @@ https://doi.org/10.1515/9783110264043
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visceral pleura
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FMA
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pleural cavity
http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png
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Wikipedia
@@ -372327,7 +372317,7 @@ https://doi.org/10.1515/9783110264043
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A double-walled sac containing the heart and the roots of the great vessels.
FMA:9868
RETIRED_EHDAA2:0001443
@@ -372341,14 +372331,14 @@ https://doi.org/10.1515/9783110264043
pericardial sac
http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png
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FMA
@@ -372372,7 +372362,7 @@ https://doi.org/10.1515/9783110264043
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pericardium
http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png
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MA
@@ -372631,7 +372621,7 @@ https://doi.org/10.1515/9783110264043
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autonomic nervous system
http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png
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EMAPA
MA
NIFSTD
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clitoris
http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg
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MA
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Wikipedia
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EHDAA2
Wikipedia
@@ -373758,7 +373748,7 @@ https://doi.org/10.1515/9783110264043
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An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues.
consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)
The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24].
@@ -373785,14 +373775,14 @@ https://doi.org/10.1515/9783110264043
oral epithelium
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AAO-modified
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visceral serous pericardium
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cjm
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FMA
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decidua
http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png
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maternal
MA
@@ -374203,7 +374193,7 @@ https://doi.org/10.1515/9783110264043
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The mucous secreting gland associated with the mucuous membrane lining the uterus.
simple or branched tubular
@@ -374231,7 +374221,7 @@ https://doi.org/10.1515/9783110264043
endometrial gland
http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png
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Wikipedia:Tubular_gland
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iris epithelium
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MA
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MP
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trabecula carnea
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WP
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@@ -375099,7 +375089,7 @@ https://doi.org/10.1515/9783110264043
https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern
http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg
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VSAO
@@ -375384,8 +375374,8 @@ https://doi.org/10.1515/9783110264043
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tunica media
https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg
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cjm
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cjm
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The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong].
the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure
the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts
@@ -375497,11 +375487,11 @@ https://doi.org/10.1515/9783110264043
tunica intima
https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg
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check for exceptions, e.g. capillaries
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ISBN:0073040584
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One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches.
One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]
A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]
@@ -376028,15 +376018,15 @@ https://doi.org/10.1515/9783110264043
pharyngeal arch
http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png
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PMID:16313389
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http://tolweb.org/Chordata/2499
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PMID:16313389
@@ -376130,7 +376120,7 @@ https://doi.org/10.1515/9783110264043
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Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic.
Do not merge with neurogenic placode
Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons
@@ -376150,7 +376140,7 @@ https://doi.org/10.1515/9783110264043
cranial placode
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@@ -376163,7 +376153,7 @@ https://doi.org/10.1515/9783110264043
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PMID:11523831
PMID:22512454
@@ -377158,7 +377148,7 @@ https://doi.org/10.1515/9783110264043
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The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate.
consider adding class for organizer. Consider adding separate class for isthmus as a structure
Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]
@@ -377207,11 +377197,11 @@ https://doi.org/10.1515/9783110264043
midbrain-hindbrain boundary
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ZFA
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ZFA
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+
+
A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis.
The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]
relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]
@@ -377307,11 +377297,11 @@ https://doi.org/10.1515/9783110264043
periderm
-
+
-
+
@@ -377324,13 +377314,13 @@ https://doi.org/10.1515/9783110264043
-
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EHDAA2
-
+
ZFA
@@ -377496,7 +377486,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -377519,7 +377509,7 @@ https://doi.org/10.1515/9783110264043
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+
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form.
Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]
It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]
@@ -377544,14 +377534,14 @@ https://doi.org/10.1515/9783110264043
presomitic mesoderm
-
+
-
+
Bgee:AN
@@ -377611,8 +377601,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP].
Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]
The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
@@ -377636,11 +377626,11 @@ https://doi.org/10.1515/9783110264043
The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150]
pronephric duct
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-
+
@@ -377653,13 +377643,13 @@ https://doi.org/10.1515/9783110264043
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Wikipedia
-
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XAO
@@ -377848,14 +377838,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
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A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue.
TODO - check; developmental relationship to anterior hypoblast in ZFA?
Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]
@@ -377880,24 +377870,24 @@ https://doi.org/10.1515/9783110264043
prechordal plate
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ZFA
-
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PMID:16313393
@@ -377954,9 +377944,9 @@ https://doi.org/10.1515/9783110264043
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+
@@ -377998,34 +377988,34 @@ https://doi.org/10.1515/9783110264043
intermediate mesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
-
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-
+
-
+
-
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AAO
-
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EMAPA
-
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XAO
@@ -378337,7 +378327,7 @@ https://doi.org/10.1515/9783110264043
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+
@@ -378375,7 +378365,7 @@ https://doi.org/10.1515/9783110264043
eye primordium
-
+
@@ -378388,7 +378378,7 @@ https://doi.org/10.1515/9783110264043
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+
PMID:16496288
XAO
@@ -378450,8 +378440,8 @@ https://doi.org/10.1515/9783110264043
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+
@@ -378480,24 +378470,24 @@ https://doi.org/10.1515/9783110264043
optic cup
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-
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ZFA
-
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ZFA
@@ -378563,7 +378553,7 @@ https://doi.org/10.1515/9783110264043
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+
@@ -378604,7 +378594,7 @@ https://doi.org/10.1515/9783110264043
lens placode
http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png
-
+
@@ -378617,7 +378607,7 @@ https://doi.org/10.1515/9783110264043
-
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ZFA
@@ -378686,7 +378676,7 @@ https://doi.org/10.1515/9783110264043
-
+
Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA].
Consider adding subclasses for male and female specific variants
TODO - mesonephric portion of the nephric duct
@@ -378724,7 +378714,7 @@ https://doi.org/10.1515/9783110264043
mesonephric duct
http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png
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+
@@ -378737,7 +378727,7 @@ https://doi.org/10.1515/9783110264043
-
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EHDAA2
@@ -378827,15 +378817,15 @@ https://doi.org/10.1515/9783110264043
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-
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+
A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA].
The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]
@@ -378867,34 +378857,34 @@ https://doi.org/10.1515/9783110264043
neural plate
https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png
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GOTAX:0000352
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Wikipedia
-
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Bgee:AN
@@ -379019,7 +379009,7 @@ https://doi.org/10.1515/9783110264043
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+
The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO].
Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]
Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]
@@ -379048,7 +379038,7 @@ https://doi.org/10.1515/9783110264043
paraxial mesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
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@@ -379061,7 +379051,7 @@ https://doi.org/10.1515/9783110264043
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Bgee:AN
@@ -379130,8 +379120,8 @@ https://doi.org/10.1515/9783110264043
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-
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+
@@ -379157,11 +379147,11 @@ https://doi.org/10.1515/9783110264043
epibranchial placode
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@@ -379175,13 +379165,13 @@ https://doi.org/10.1515/9783110264043
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ZFA
-
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EHDAA2-abduced
@@ -379284,7 +379274,7 @@ https://doi.org/10.1515/9783110264043
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@@ -379328,7 +379318,7 @@ https://doi.org/10.1515/9783110264043
lateral plate mesoderm
http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png
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@@ -379341,7 +379331,7 @@ https://doi.org/10.1515/9783110264043
-
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EHDAA2
VHOG
@@ -379425,7 +379415,7 @@ https://doi.org/10.1515/9783110264043
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@@ -379468,7 +379458,7 @@ https://doi.org/10.1515/9783110264043
myotome
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png
-
+
@@ -379481,7 +379471,7 @@ https://doi.org/10.1515/9783110264043
-
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EHDAA2-abduced
@@ -379544,7 +379534,7 @@ https://doi.org/10.1515/9783110264043
-
+
Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia].
Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
@@ -379564,14 +379554,14 @@ https://doi.org/10.1515/9783110264043
trunk neural crest
-
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-
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ZFA
@@ -379614,15 +379604,15 @@ https://doi.org/10.1515/9783110264043
-
-
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+
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Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone.
should probably be merged with heart rudiment.
Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]
@@ -379642,15 +379632,15 @@ https://doi.org/10.1515/9783110264043
heart primordium
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-
+
-
+
@@ -379663,19 +379653,19 @@ https://doi.org/10.1515/9783110264043
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ZFA
-
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ZFA
-
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XAO
@@ -379813,8 +379803,8 @@ https://doi.org/10.1515/9783110264043
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+
Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP].
Skeletogenic portion of somites.[AAO]
The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]
@@ -379842,11 +379832,11 @@ https://doi.org/10.1515/9783110264043
sclerotome
http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png
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-
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@@ -379865,13 +379855,13 @@ https://doi.org/10.1515/9783110264043
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VHOG:0000680
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ZFA
@@ -381200,8 +381190,8 @@ https://doi.org/10.1515/9783110264043
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@@ -381249,24 +381239,24 @@ https://doi.org/10.1515/9783110264043
chorion membrane
http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png
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-
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-
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Hymans
-
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ISBN:0073040584
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@@ -381917,14 +381907,14 @@ https://doi.org/10.1515/9783110264043
Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"]
metanephric mesenchyme
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ISBN:9780878932504
@@ -381988,14 +381978,14 @@ https://doi.org/10.1515/9783110264043
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An extraembryonic structure that develops_from a syncytiotrophoblast and is part of a chorion.
TODO - check
EHDAA2:0001973
@@ -382004,24 +381994,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0003224
chorion syncytiotrophoblast
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+
-
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-
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EHDAA2
-
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polar trophectoderm syncytiotrophoblast
EHDAA2
@@ -382427,7 +382417,7 @@ https://doi.org/10.1515/9783110264043
-
+
A mesenchyme that is part of a chorion.
TODO - check
UBERON:0003423
@@ -382446,7 +382436,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0003265
chorionic mesenchyme
-
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@@ -382465,7 +382455,7 @@ https://doi.org/10.1515/9783110264043
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ISBN:0073040584
@@ -382673,8 +382663,8 @@ https://doi.org/10.1515/9783110264043
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@@ -382706,24 +382696,24 @@ https://doi.org/10.1515/9783110264043
skeleton of lower jaw
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EHDAA2
-
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VHOG-modified
@@ -382799,12 +382789,12 @@ https://doi.org/10.1515/9783110264043
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@@ -382831,7 +382821,7 @@ https://doi.org/10.1515/9783110264043
mesentery of stomach
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@@ -382844,7 +382834,7 @@ https://doi.org/10.1515/9783110264043
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MA
@@ -383156,13 +383146,13 @@ https://doi.org/10.1515/9783110264043
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-
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Racemose mucous glands beneath the mucous membrane of the pharynx.
BTO:0004849
EHDAA2:0001461
@@ -383175,14 +383165,14 @@ https://doi.org/10.1515/9783110264043
pharyngeal gland
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-
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BTO
@@ -383291,7 +383281,7 @@ https://doi.org/10.1515/9783110264043
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A blood island that is part of a mesoderm.
in EHDAA2, gives rise to blood and dorsal aorta
UBERON:0003305
@@ -383304,7 +383294,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0003304
mesoderm blood island
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EHDAA2
@@ -383416,7 +383406,7 @@ https://doi.org/10.1515/9783110264043
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Mesenchyme that is part of a developing camera-type eye.
TODO - change mesenchyme relationships to precursor_of
EHDAA2:0000485
@@ -383428,14 +383418,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003314
eye mesenchyme
-
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-
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EHDAA2
@@ -383628,7 +383618,7 @@ https://doi.org/10.1515/9783110264043
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Mesenchyme that is part of a developing upper jaw [Automatically generated definition].
EHDAA2:0002124
EHDAA:8031
@@ -383641,14 +383631,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003323
mesenchyme of upper jaw
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-
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EHDAA2
@@ -383699,7 +383689,7 @@ https://doi.org/10.1515/9783110264043
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Mesenchyme that is part of a developing lower jaw [Automatically generated definition].
EHDAA2:0001024
EHDAA:8003
@@ -383712,14 +383702,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003324
mesenchyme of lower jaw
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-
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EHDAA2
@@ -385111,15 +385101,15 @@ https://doi.org/10.1515/9783110264043
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+
-
An epithelium that is part of a pharynx [Automatically generated definition].
Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]
BSA:0000112
@@ -385139,24 +385129,24 @@ https://doi.org/10.1515/9783110264043
pharyngeal epithelium
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ZFA
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ZFA
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An epithelium that is part of a midgut.
BTO:0005053
EHDAA2:0001195
@@ -385226,14 +385216,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003352
epithelium of midgut
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BTO
@@ -385526,7 +385516,7 @@ https://doi.org/10.1515/9783110264043
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@@ -385539,7 +385529,7 @@ https://doi.org/10.1515/9783110264043
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An unilaminar epithelium that surrounds a pelvic appendage bud.
UBERON:0005232
EHDAA2:0001034
@@ -385555,24 +385545,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0003371
pelvic appendage bud ectoderm
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EHDAA2
-
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EHDAA2
@@ -385640,7 +385630,7 @@ https://doi.org/10.1515/9783110264043
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An unilaminar epithelium that surrounds a pectoral appendage bud.
UBERON:0005231
UBERON:0005663
@@ -385670,24 +385660,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0003372
pectoral appendage bud ectoderm
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EHDAA2
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EHDAA2
@@ -385751,7 +385741,7 @@ https://doi.org/10.1515/9783110264043
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An extraembryonic structure that develops_from a ectoderm and is part of a chorion.
BTO:0005145
EMAPA:16113
@@ -385773,14 +385763,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003374
chorionic ectoderm
-
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-
+
ISBN:0073040584
@@ -387229,7 +387219,7 @@ https://doi.org/10.1515/9783110264043
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A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP].
TODO - check
@@ -387244,14 +387234,14 @@ https://doi.org/10.1515/9783110264043
mesenchyme of umbilical cord
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Wikipedia
@@ -388260,13 +388250,13 @@ https://doi.org/10.1515/9783110264043
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A bone that is part of a facial skeleton [Automatically generated definition].
test whether 'facial bone' is an exact synonym
EMAPA:19019
@@ -388287,14 +388277,14 @@ https://doi.org/10.1515/9783110264043
facial bone
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-
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MA
@@ -388447,14 +388437,14 @@ https://doi.org/10.1515/9783110264043
-
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-
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The ureteral branches of renal artery are small branches which supply the ureter.
ureteric artery
@@ -388468,24 +388458,24 @@ https://doi.org/10.1515/9783110264043
ureteric segment of renal artery
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FMA
-
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FMA
@@ -388569,7 +388559,7 @@ https://doi.org/10.1515/9783110264043
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The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose.
EMAPA:37430
@@ -388586,14 +388576,14 @@ https://doi.org/10.1515/9783110264043
artery of upper lip
-
+
-
+
FMA
@@ -388659,7 +388649,7 @@ https://doi.org/10.1515/9783110264043
-
+
The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery.
EMAPA:37429
@@ -388677,14 +388667,14 @@ https://doi.org/10.1515/9783110264043
artery of lower lip
-
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-
+
FMA
@@ -389310,7 +389300,7 @@ https://doi.org/10.1515/9783110264043
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+
An endothelium of capillary that is part of a respiratory system [Automatically generated definition].
EMAPA:37575
MA:0001808
@@ -389341,14 +389331,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003489
respiratory system capillary endothelium
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -389580,7 +389570,7 @@ https://doi.org/10.1515/9783110264043
-
+
An arteriole that is part of a respiratory system [Automatically generated definition].
EMAPA:37568
MA:0001803
@@ -389588,14 +389578,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003495
respiratory system arteriole
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -389629,7 +389619,7 @@ https://doi.org/10.1515/9783110264043
-
+
A blood vessel that is part of a head [Automatically generated definition].
EMAPA:36610
MA:0000575
@@ -389641,14 +389631,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003496
head blood vessel
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -393869,12 +393859,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
@@ -393901,7 +393891,7 @@ https://doi.org/10.1515/9783110264043
intrahepatic bile duct
-
+
@@ -393914,7 +393904,7 @@ https://doi.org/10.1515/9783110264043
-
+
MA
@@ -394477,7 +394467,7 @@ https://doi.org/10.1515/9783110264043
-
+
The central part of the thoracic cavity enclosed by the left and right pleurae.
mediastinal
CALOHA:TS-2338
@@ -394499,14 +394489,14 @@ https://doi.org/10.1515/9783110264043
mediastinum
http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png
-
+
-
+
FMA
@@ -395026,7 +395016,7 @@ https://doi.org/10.1515/9783110264043
-
+
Any muscle organ that is part of a thorax [Automatically generated definition].
MA:0000561
muscle organ of thorax
@@ -395036,14 +395026,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003830
thoracic segment muscle
-
+
-
+
prolog
@@ -395155,7 +395145,7 @@ https://doi.org/10.1515/9783110264043
-
+
Any muscle organ that is part of a esophagus [Automatically generated definition].
merge muscle and muscle layer?
EMAPA:26983
@@ -395172,14 +395162,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003832
esophagus muscle
-
+
-
+
MA
@@ -396044,12 +396034,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
A neural plate that develops_from a future spinal cord.
Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]
@@ -396062,14 +396052,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003854
spinal cord neural plate
-
+
-
+
ZFA
@@ -396322,7 +396312,7 @@ https://doi.org/10.1515/9783110264043
-
+
The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom.
consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults
(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]
@@ -396338,14 +396328,14 @@ https://doi.org/10.1515/9783110264043
intraembryonic coelom
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-
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Wikipedia
@@ -396413,7 +396403,7 @@ https://doi.org/10.1515/9783110264043
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@@ -396472,14 +396462,14 @@ https://doi.org/10.1515/9783110264043
fallopian tube
http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg
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+
-
+
FMA-abduced-lr
@@ -396554,7 +396544,7 @@ https://doi.org/10.1515/9783110264043
-
+
Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM].
Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]
Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]
@@ -396584,14 +396574,14 @@ https://doi.org/10.1515/9783110264043
Mullerian duct
http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png
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-
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Wikipedia
@@ -396713,8 +396703,8 @@ https://doi.org/10.1515/9783110264043
-
-
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+
@@ -396748,11 +396738,11 @@ https://doi.org/10.1515/9783110264043
liver primordium
-
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-
+
@@ -396771,13 +396761,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
ventral foregut endoderm
Zaret 1996
@@ -396900,7 +396890,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -396920,14 +396910,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0003898
skeletal muscle tissue of trunk
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -396988,7 +396978,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -397011,7 +397001,7 @@ https://doi.org/10.1515/9783110264043
-
+
The part of the retina that contains neurons and photoreceptor cells[GO].
(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]
@@ -397043,14 +397033,14 @@ https://doi.org/10.1515/9783110264043
retinal neural layer
-
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-
+
Bgee:AN
@@ -397370,7 +397360,7 @@ https://doi.org/10.1515/9783110264043
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@@ -397400,14 +397390,14 @@ https://doi.org/10.1515/9783110264043
pancreas primordium
http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png
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-
+
Wikipedia
@@ -397449,16 +397439,16 @@ https://doi.org/10.1515/9783110264043
-
-
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-
-
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+
The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID].
EFO:0003470
EMAPA:35645
@@ -397479,19 +397469,19 @@ https://doi.org/10.1515/9783110264043
http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg
http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png
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-
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-
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-
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@@ -397504,26 +397494,26 @@ https://doi.org/10.1515/9783110264043
-
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EHDAA2
-
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Wikipedia:Pancreas#Embryological_development
-
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zebrafish
Wikipedia:Pancreatic_bud
-
+
EHDAA2-inferred
@@ -397565,8 +397555,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
Pancreatic bud that gives rise to the accessory pancreatic duct.
The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]
In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]
@@ -397594,24 +397584,24 @@ https://doi.org/10.1515/9783110264043
dorsal pancreatic bud
http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png
-
+
-
+
-
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EHDAA2
-
+
XAO
@@ -397658,8 +397648,8 @@ https://doi.org/10.1515/9783110264043
-
-
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+
Pancreatic bud that gives rise to the major pancreatic duct.
In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]
The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]
@@ -397687,24 +397677,24 @@ https://doi.org/10.1515/9783110264043
ventral pancreatic bud
http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png
-
+
-
+
-
+
EHDAA2
-
+
PMID:16417468
WP
@@ -398438,7 +398428,7 @@ https://doi.org/10.1515/9783110264043
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@@ -398475,14 +398465,14 @@ https://doi.org/10.1515/9783110264043
rete testis
http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg
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+
-
+
Wikipedia
@@ -398901,7 +398891,7 @@ https://doi.org/10.1515/9783110264043
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+
A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells.
Not to be confused with 'dermatome segment of skin'.
AAO:0011028
@@ -398928,7 +398918,7 @@ https://doi.org/10.1515/9783110264043
dermatome
http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png
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@@ -398941,7 +398931,7 @@ https://doi.org/10.1515/9783110264043
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EHDAA2-abduced
@@ -399260,7 +399250,7 @@ https://doi.org/10.1515/9783110264043
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@@ -399287,14 +399277,14 @@ https://doi.org/10.1515/9783110264043
biliary ductule
-
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-
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BTO
@@ -399385,7 +399375,7 @@ https://doi.org/10.1515/9783110264043
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The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium.
consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure
The layer of undifferentiated, proliferating cells that line the neural tube lumen
@@ -399403,7 +399393,7 @@ https://doi.org/10.1515/9783110264043
neural tube ventricular layer
-
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@@ -399416,7 +399406,7 @@ https://doi.org/10.1515/9783110264043
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NCBIBook:NBK10047
@@ -399477,7 +399467,7 @@ https://doi.org/10.1515/9783110264043
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@@ -399501,7 +399491,7 @@ https://doi.org/10.1515/9783110264043
neural tube mantle layer
-
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@@ -399514,7 +399504,7 @@ https://doi.org/10.1515/9783110264043
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+
by division
NCBIBook:NBK10047
@@ -399552,7 +399542,7 @@ https://doi.org/10.1515/9783110264043
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@@ -399569,14 +399559,14 @@ https://doi.org/10.1515/9783110264043
neural tube marginal layer
-
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forms from axons
@@ -399618,7 +399608,7 @@ https://doi.org/10.1515/9783110264043
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@@ -399643,14 +399633,14 @@ https://doi.org/10.1515/9783110264043
neural tube basal plate
-
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-
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Shh
Swenson
@@ -399765,7 +399755,7 @@ https://doi.org/10.1515/9783110264043
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The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it.
Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity.
EHDAA2:0001076
@@ -399799,24 +399789,24 @@ https://doi.org/10.1515/9783110264043
medial nasal prominence
http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png
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-
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EHDAA2
-
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Wikipedia
@@ -400657,7 +400647,7 @@ https://doi.org/10.1515/9783110264043
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A myocardium trabecular layer that is part of a cardiac ventricle.
TODO - check FMA
FMA:83511
@@ -400671,14 +400661,14 @@ https://doi.org/10.1515/9783110264043
trabecular layer of ventricle
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -400713,9 +400703,9 @@ https://doi.org/10.1515/9783110264043
-
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-
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@@ -400748,34 +400738,34 @@ https://doi.org/10.1515/9783110264043
optic vesicle
http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png
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ZFA
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GO-def
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ZFA
@@ -400924,8 +400914,8 @@ https://doi.org/10.1515/9783110264043
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A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle.
this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]
XAO:0004185
@@ -400938,24 +400928,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0004140
primary heart field
-
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-
+
-
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GO:0003128
-
+
https://orcid.org/0000-0003-3308-6245
@@ -401020,7 +401010,7 @@ https://doi.org/10.1515/9783110264043
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An epithelial tube that will give rise to the mature heart.
the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube.
AAO:0010411
@@ -401040,14 +401030,14 @@ https://doi.org/10.1515/9783110264043
heart tube
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ZFA-modified
@@ -401192,8 +401182,8 @@ https://doi.org/10.1515/9783110264043
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The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles.
the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles.
HPS
@@ -401204,11 +401194,11 @@ https://doi.org/10.1515/9783110264043
UBERON:0004146
His-Purkinje system
-
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@@ -401221,13 +401211,13 @@ https://doi.org/10.1515/9783110264043
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GO
-
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PMID:12626327
PMID:21234997
github:michaelerice
@@ -401408,8 +401398,8 @@ https://doi.org/10.1515/9783110264043
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+
An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium.
propepicardial
Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]
@@ -401421,24 +401411,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0004160
proepicardium
-
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-
+
-
+
todo check other taxa
-
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ZFA
@@ -402320,8 +402310,8 @@ https://doi.org/10.1515/9783110264043
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A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition].
MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa
EMAPA:35469
@@ -402337,24 +402327,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0004220
large intestine smooth muscle
-
+
-
+
-
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MA
-
+
consider merging
@@ -402435,7 +402425,7 @@ https://doi.org/10.1515/9783110264043
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@@ -402472,14 +402462,14 @@ https://doi.org/10.1515/9783110264043
intestine smooth muscle
-
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consider merging
@@ -403863,7 +403853,7 @@ https://doi.org/10.1515/9783110264043
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A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition].
MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa
EMAPA:35783
@@ -403888,14 +403878,14 @@ https://doi.org/10.1515/9783110264043
small intestine smooth muscle
-
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-
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consider merging
@@ -404756,13 +404746,13 @@ https://doi.org/10.1515/9783110264043
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-
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eye muscle
-
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MA
@@ -404874,7 +404864,7 @@ https://doi.org/10.1515/9783110264043
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The bilaminar epithelium formed from the myotome and dermatome.
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768].
Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]
@@ -404897,7 +404887,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0004290
dermomyotome
-
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@@ -404916,7 +404906,7 @@ https://doi.org/10.1515/9783110264043
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EHDAA2
ZFA
@@ -405198,11 +405188,11 @@ https://doi.org/10.1515/9783110264043
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-
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A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG].
A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]
Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]
@@ -405227,55 +405217,55 @@ https://doi.org/10.1515/9783110264043
allantois
http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png
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-
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EHDAA2-modified
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Hymans
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Hymans
-
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hindgut diverticulum endoderm
ISBN:0073040584
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ISBN:0073040584
@@ -405422,14 +405412,14 @@ https://doi.org/10.1515/9783110264043
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Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition.
distinction between trophectoderm and trophoblast unclear/inconsistent in many sources
The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]
@@ -405447,11 +405437,11 @@ https://doi.org/10.1515/9783110264043
trophectoderm
-
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EHDAA2
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EHDAA2
@@ -405873,7 +405863,7 @@ https://doi.org/10.1515/9783110264043
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pharyngeal arch artery
http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png
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-
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ZFA
@@ -406188,7 +406178,7 @@ https://doi.org/10.1515/9783110264043
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A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP].
Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]
@@ -406220,14 +406210,14 @@ https://doi.org/10.1515/9783110264043
Descemet's membrane
https://github.com/obophenotype/uberon/issues/15
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-
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Cline et al
@@ -407645,12 +407635,12 @@ https://doi.org/10.1515/9783110264043
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A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition].
Note placement of MA class based on parthood relationship
EMAPA:32688
@@ -407661,14 +407651,14 @@ https://doi.org/10.1515/9783110264043
cardiac muscle tissue of myocardium
-
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-
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MA
@@ -407855,21 +407845,21 @@ https://doi.org/10.1515/9783110264043
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A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition].
FMA:84429
uberon
UBERON:0004525
cardiac muscle tissue of trabecula carnea of right ventricle
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -407898,21 +407888,21 @@ https://doi.org/10.1515/9783110264043
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+
A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition].
FMA:84430
uberon
UBERON:0004526
cardiac muscle tissue of trabecula carnea of left ventricle
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -408898,7 +408888,7 @@ https://doi.org/10.1515/9783110264043
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+
@@ -408932,7 +408922,7 @@ https://doi.org/10.1515/9783110264043
liver lobule
-
+
@@ -408945,7 +408935,7 @@ https://doi.org/10.1515/9783110264043
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+
FMA
MA
@@ -409211,7 +409201,7 @@ https://doi.org/10.1515/9783110264043
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@@ -409243,14 +409233,14 @@ https://doi.org/10.1515/9783110264043
interventricular septum membranous part
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+
Wikipedia
@@ -409457,8 +409447,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane.
BAMS:RA
EMAPA:35721
@@ -409487,25 +409477,25 @@ https://doi.org/10.1515/9783110264043
raphe nuclei
http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png
-
+
-
+
-
+
GO
Wikipedia
-
+
Wikipedia
@@ -410062,7 +410052,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -410074,7 +410064,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -410105,7 +410095,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -410128,11 +410118,11 @@ https://doi.org/10.1515/9783110264043
paired limb/fin
-
+
-
+
@@ -410145,13 +410135,13 @@ https://doi.org/10.1515/9783110264043
-
+
VSAO
-
+
definitional
@@ -410233,7 +410223,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -410255,14 +410245,14 @@ https://doi.org/10.1515/9783110264043
pelvic appendage
-
+
-
+
definitional
@@ -410331,7 +410321,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -410355,14 +410345,14 @@ https://doi.org/10.1515/9783110264043
pectoral appendage
-
+
-
+
definitional
@@ -410904,8 +410894,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -410920,25 +410910,25 @@ https://doi.org/10.1515/9783110264043
UBERON:0004737
metanephric collecting duct
-
+
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
-
+
Wikipedia-abduced
@@ -410966,7 +410956,7 @@ https://doi.org/10.1515/9783110264043
-
+
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO].
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
EMAPA:37744
@@ -410980,7 +410970,7 @@ https://doi.org/10.1515/9783110264043
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
skeletal tissue
-
+
@@ -410993,7 +410983,7 @@ https://doi.org/10.1515/9783110264043
-
+
2012-08-14
VSAO:0000015
VSAO
@@ -411165,7 +411155,7 @@ https://doi.org/10.1515/9783110264043
-
+
The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP].
in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)
AAO:0000094
@@ -411187,7 +411177,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0004761
cartilaginous neurocranium
-
+
@@ -411200,7 +411190,7 @@ https://doi.org/10.1515/9783110264043
-
+
PMC1571569
@@ -411297,7 +411287,7 @@ https://doi.org/10.1515/9783110264043
-
+
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
@@ -411313,14 +411303,14 @@ https://doi.org/10.1515/9783110264043
skeletal element
-
+
-
+
VSAO
@@ -411449,7 +411439,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -411488,14 +411478,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004770
articular system
-
+
-
+
FMA
@@ -411610,7 +411600,7 @@ https://doi.org/10.1515/9783110264043
-
+
A lamina propria that is part of a respiratory system [Automatically generated definition].
EMAPA:37576
MA:0001821
@@ -411625,14 +411615,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004779
respiratory system lamina propria
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -411708,7 +411698,7 @@ https://doi.org/10.1515/9783110264043
-
+
A lamina propria that is part of a gastrointestinal system.
MA:0001899
NCIT:C49299
@@ -411717,14 +411707,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004780
gastrointestinal system lamina propria
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -411759,7 +411749,7 @@ https://doi.org/10.1515/9783110264043
-
+
A lamina propria that is part of a gallbladder [Automatically generated definition].
EMAPA:35371
FMA:278594
@@ -411778,14 +411768,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004781
gallbladder lamina propria
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -412380,10 +412370,10 @@ https://doi.org/10.1515/9783110264043
-
-
-
-
+
+
+
+
A mucosa that is part of a gastrointestinal system.
BTO:0000546
BTO:0005568
@@ -412399,44 +412389,44 @@ https://doi.org/10.1515/9783110264043
The gut mucosa of amphioxus has insulin-secreting cells. http://www.ncbi.nlm.nih.gov/pubmed/16417468
gastrointestinal system mucosa
-
+
-
+
-
+
-
+
-
+
PMID:16417468
-
+
PMID:16417468
-
+
PMID:16417468
-
+
BTO-modified
@@ -414762,7 +414752,7 @@ https://doi.org/10.1515/9783110264043
-
+
An endothelium of artery that is part of a respiratory system [Automatically generated definition].
EMAPA:37566
@@ -414783,14 +414773,14 @@ https://doi.org/10.1515/9783110264043
respiratory system arterial endothelium
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -415724,7 +415714,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -415747,14 +415737,14 @@ https://doi.org/10.1515/9783110264043
splanchnopleure
http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png
-
+
-
+
EHDAA2
@@ -415782,7 +415772,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -415805,14 +415795,14 @@ https://doi.org/10.1515/9783110264043
somatopleure
http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png
-
+
-
+
EHDAA2
@@ -415878,9 +415868,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
@@ -415901,34 +415891,34 @@ https://doi.org/10.1515/9783110264043
urogenital fold
-
+
-
+
-
+
-
+
EHDAA2
-
+
Wikipedia
-
+
EHDAA2
@@ -416118,7 +416108,7 @@ https://doi.org/10.1515/9783110264043
-
+
The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra.
we follow EHDAA2 in dividing the UGS into epithelium and lumen
EHDAA2:0004061
@@ -416129,14 +416119,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004902
urogenital sinus epithelium
-
+
-
+
EHDAA2
@@ -416612,8 +416602,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
EHDAA2:0000171
EMAPA:16561
EMAPA_RETIRED:16565
@@ -416624,11 +416614,11 @@ https://doi.org/10.1515/9783110264043
biliary bud
http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png
-
+
-
+
@@ -416641,13 +416631,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
EHDAA2-modified
@@ -417818,7 +417808,7 @@ https://doi.org/10.1515/9783110264043
-
+
The submucous layer of the wall of the urinary bladder.
BTO:0002117
@@ -417837,14 +417827,14 @@ https://doi.org/10.1515/9783110264043
submucosa of urinary bladder
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -417918,7 +417908,7 @@ https://doi.org/10.1515/9783110264043
-
+
A mucosa that is part of a ureter [Automatically generated definition].
FMA:15894
SCTID:40476001
@@ -417939,14 +417929,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004980
mucosa of ureter
-
+
-
+
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -419060,7 +419050,7 @@ https://doi.org/10.1515/9783110264043
-
+
A mucosa that is part of a pyloric antrum [Automatically generated definition].
BTO:0004107
FMA:17055
@@ -419093,14 +419083,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0004997
mucosa of pyloric antrum
-
+
-
+
BTO
@@ -422043,20 +422033,20 @@ https://doi.org/10.1515/9783110264043
-
+
Missing definition for term UBERON:0005064. Please replace it using linked reference.
uberon
UBERON:0005064
left ventricular trabecular myocardium
-
+
-
+
GO
@@ -422083,20 +422073,20 @@ https://doi.org/10.1515/9783110264043
-
+
Missing definition for term UBERON:0005066. Please replace it using linked reference.
uberon
UBERON:0005066
right ventricular trabecular myocardium
-
+
-
+
GO
@@ -422456,7 +422446,7 @@ https://doi.org/10.1515/9783110264043
-
+
Missing definition for term UBERON:0005095. Please replace it using linked reference.
class added for consistency with GO - consider merging with kidney mesenchyme.
uberon
@@ -422464,14 +422454,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005095
kidney rudiment
-
+
-
+
GO
@@ -422662,14 +422652,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
A metanephric nephron is the functional unit of the metanephros[GO].
The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]
UBERON:0005142
@@ -422678,25 +422668,25 @@ https://doi.org/10.1515/9783110264043
UBERON:0005110
metanephric nephron
-
+
-
+
-
+
Wikipedia
Wikipedia:Nephron
-
+
Bgee:AN
@@ -422723,20 +422713,20 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2:0001140
uberon
UBERON:0005113
metanephric cortex mesenchyme
-
+
-
+
EHDAA2
@@ -422758,32 +422748,32 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO].
uberon
UBERON:0005115
metanephric cortical collecting duct
-
+
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -422812,20 +422802,20 @@ https://doi.org/10.1515/9783110264043
-
+
The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO].
uberon
UBERON:0005134
metanephric nephron epithelium
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -422892,7 +422882,7 @@ https://doi.org/10.1515/9783110264043
-
+
A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO].
UBERON:0005128
UBERON:0005152
@@ -422900,14 +422890,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005146
metanephric nephron tubule
-
+
-
+
ISBN:9780878932504
@@ -422935,7 +422925,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -422951,14 +422941,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005147
metanephric renal vesicle
-
+
-
+
EHDAA2
@@ -423698,7 +423688,7 @@ https://doi.org/10.1515/9783110264043
-
+
An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP].
EMAPA:37513
@@ -423715,14 +423705,14 @@ https://doi.org/10.1515/9783110264043
deferent duct artery
-
+
-
+
Wikipedia
@@ -424498,7 +424488,7 @@ https://doi.org/10.1515/9783110264043
-
+
Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells.
Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]
EFO:0003492
@@ -424520,14 +424510,14 @@ https://doi.org/10.1515/9783110264043
head mesenchyme
-
+
-
+
EHDAA2
@@ -424594,7 +424584,7 @@ https://doi.org/10.1515/9783110264043
-
+
Mesenchyme that is part of a developing trunk.
EFO:0003485
EHDAA2:0002092
@@ -424610,14 +424600,14 @@ https://doi.org/10.1515/9783110264043
trunk mesenchyme
-
+
-
+
EHDAA2
@@ -424657,7 +424647,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -424681,14 +424671,14 @@ https://doi.org/10.1515/9783110264043
renal cortex artery
-
+
-
+
MA
@@ -424740,7 +424730,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -424763,14 +424753,14 @@ https://doi.org/10.1515/9783110264043
renal cortex vein
-
+
-
+
MA
@@ -424801,14 +424791,14 @@ https://doi.org/10.1515/9783110264043
-
+
+
-
@@ -424834,24 +424824,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0005270
renal cortex interstitium
-
+
-
+
-
+
MA
-
+
MA
@@ -424891,7 +424881,7 @@ https://doi.org/10.1515/9783110264043
-
+
The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP].
The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]
@@ -424916,14 +424906,14 @@ https://doi.org/10.1515/9783110264043
myelencephalon
http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg
-
+
-
+
definitional
@@ -425291,7 +425281,7 @@ https://doi.org/10.1515/9783110264043
-
+
The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP].
TODO - check primary vs testis
EHDAA2:0002011
@@ -425308,14 +425298,14 @@ https://doi.org/10.1515/9783110264043
testis sex cord
-
+
-
+
Bgee:AN
@@ -425433,13 +425423,13 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO].
Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]
@@ -425452,14 +425442,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005310
pronephric nephron tubule
-
+
-
+
GO
@@ -425607,7 +425597,7 @@ https://doi.org/10.1515/9783110264043
-
+
The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO].
AAO:0010390
XAO:0000151
@@ -425615,14 +425605,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005319
mesonephric collecting duct
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -425692,7 +425682,7 @@ https://doi.org/10.1515/9783110264043
-
+
A nephron that is part of a mesonephros.
The structure that is the basic functional unit of the kidney.[AAO]
AAO:0010387
@@ -425704,14 +425694,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005322
mesonephric nephron
-
+
-
+
XAO
@@ -425795,20 +425785,20 @@ https://doi.org/10.1515/9783110264043
-
+
The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO].
uberon
UBERON:0005330
mesonephric nephron epithelium
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -425837,7 +425827,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -425852,14 +425842,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005331
mesonephric renal vesicle
-
+
-
+
ZFA
@@ -426730,7 +426720,7 @@ https://doi.org/10.1515/9783110264043
-
+
An apical ectodermal ridge that is part of a pectoral appendage bud.
An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]
@@ -426757,14 +426747,14 @@ https://doi.org/10.1515/9783110264043
pectoral appendage apical ectodermal ridge
-
+
-
+
EHDAA2
@@ -426881,7 +426871,7 @@ https://doi.org/10.1515/9783110264043
-
+
An apical ectodermal ridge that is part of a pelvic appendage bud.
An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]
Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]
@@ -426904,14 +426894,14 @@ https://doi.org/10.1515/9783110264043
pelvic appendage apical ectodermal ridge
-
+
-
+
EHDAA2
@@ -427237,7 +427227,7 @@ https://doi.org/10.1515/9783110264043
-
+
Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea.
TAO:0002188
ZFA:0001688
@@ -427245,7 +427235,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0005427
corneal primordium
-
+
@@ -427264,7 +427254,7 @@ https://doi.org/10.1515/9783110264043
-
+
ZFA
@@ -427364,7 +427354,7 @@ https://doi.org/10.1515/9783110264043
-
+
The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates.
the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac].
EHDAA2:0004145
@@ -427379,7 +427369,7 @@ https://doi.org/10.1515/9783110264043
aortic sac
-
+
@@ -427392,7 +427382,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -427726,7 +427716,7 @@ https://doi.org/10.1515/9783110264043
-
+
A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD].
sulcus limitans
BAMS:slim
@@ -427737,14 +427727,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005478
sulcus limitans of neural tube
-
+
-
+
EHDAA2
@@ -428018,7 +428008,7 @@ https://doi.org/10.1515/9783110264043
-
+
Multi-tissue structure that arises from the heart rudiment and will become the heart tube.
BTO:0006179
EHDAA2:0001512
@@ -428037,14 +428027,14 @@ https://doi.org/10.1515/9783110264043
primitive heart tube
-
+
-
+
ZFA
@@ -428126,7 +428116,7 @@ https://doi.org/10.1515/9783110264043
-
+
Cranial neural crest which gives rise to the trigeminal ganglion.
todo - compare ZFA and EHDAA2 representation
We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]
@@ -428143,7 +428133,7 @@ https://doi.org/10.1515/9783110264043
trigeminal neural crest
-
+
@@ -428162,7 +428152,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -428188,7 +428178,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -428217,7 +428207,7 @@ https://doi.org/10.1515/9783110264043
gonad primordium
-
+
@@ -428230,7 +428220,7 @@ https://doi.org/10.1515/9783110264043
-
+
ZFA
@@ -428288,15 +428278,15 @@ https://doi.org/10.1515/9783110264043
-
+
-
-
+
+
Somite located in the head region, caudal to the otic vesicle.
in humans this includes somites 1-4
They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)
@@ -428310,24 +428300,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0005594
head somite
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -428374,7 +428364,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -428394,7 +428384,7 @@ https://doi.org/10.1515/9783110264043
lung primordium
-
+
@@ -428407,7 +428397,7 @@ https://doi.org/10.1515/9783110264043
-
+
XAO
@@ -428480,8 +428470,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum.
The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]
EHDAA2:0000416
@@ -428497,11 +428487,11 @@ https://doi.org/10.1515/9783110264043
UBERON:0005602
dorsal mesogastrium
-
+
-
+
@@ -428514,13 +428504,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
EHDAA2
@@ -428558,8 +428548,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
EMAPA:16844
MA:0001636
VHOG:0000215
@@ -428569,24 +428559,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0005604
extrahepatic part of hepatic duct
-
+
-
+
-
+
MA
-
+
MA
@@ -429275,13 +429265,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2:0000314
uberon
UBERON:0005667
connecting stalk mesoderm
-
+
@@ -429294,7 +429284,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -429802,7 +429792,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -429815,7 +429805,7 @@ https://doi.org/10.1515/9783110264043
-
+
A mesoderm that has the potential to develop into a pronephros.
Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]
AAO:0011090
@@ -429834,24 +429824,24 @@ https://doi.org/10.1515/9783110264043
the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney
pronephric mesoderm
-
+
-
+
-
+
ZFA
-
+
Bgee:AN
@@ -429938,7 +429928,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2:0000474
EMAPA:31862
EMAPA:31863
@@ -429950,7 +429940,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0005728
extraembryonic mesoderm
-
+
@@ -429963,7 +429953,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -430101,7 +430091,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -430117,14 +430107,14 @@ https://doi.org/10.1515/9783110264043
paired limb/fin field
-
+
-
+
ISBN:9780878932504
ZFA-inferred
@@ -431060,7 +431050,7 @@ https://doi.org/10.1515/9783110264043
-
+
A delimited region of dense mesenchyme within looser mesenchyme.
AEO:0000148
EHDAA2_RETIRED:0003148
@@ -431070,7 +431060,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0005856
developing mesenchymal condensation
-
+
@@ -431089,7 +431079,7 @@ https://doi.org/10.1515/9783110264043
-
+
AEO-modified-relation
@@ -431111,7 +431101,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -431132,7 +431122,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0005863
cartilaginous condensation
-
+
@@ -431145,7 +431135,7 @@ https://doi.org/10.1515/9783110264043
-
+
AEO
@@ -431196,7 +431186,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -431218,14 +431208,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005865
pre-muscle condensation
-
+
-
+
AEO
@@ -431236,7 +431226,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -431256,7 +431246,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0005866
pre-cartilage condensation
-
+
@@ -431269,7 +431259,7 @@ https://doi.org/10.1515/9783110264043
-
+
AEO
@@ -431418,8 +431408,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -431458,24 +431448,24 @@ https://doi.org/10.1515/9783110264043
undifferentiated genital tubercle
http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png
-
+
-
+
-
+
EHDAA2
-
+
https://github.com/obophenotype/uberon/issues/1230
@@ -431563,8 +431553,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
The epithelial lining of the surface of the coelom.
EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium'
Wikipedia:Coelomic_epithelium
@@ -431575,24 +431565,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0005891
coelomic epithelium
-
+
-
+
-
+
XAO
-
+
XAO
@@ -432029,7 +432019,7 @@ https://doi.org/10.1515/9783110264043
-
+
trabecula
trabecular cartilage
EFO:0003677
@@ -432041,7 +432031,7 @@ https://doi.org/10.1515/9783110264043
neurocranial trabecula
-
+
@@ -432054,7 +432044,7 @@ https://doi.org/10.1515/9783110264043
-
+
ZFA
@@ -432156,7 +432146,7 @@ https://doi.org/10.1515/9783110264043
-
+
Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk.
infundibulum
EMAPA:37926
@@ -432179,14 +432169,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0005953
outflow part of right ventricle
-
+
-
+
PMID:17276708
@@ -432501,7 +432491,7 @@ https://doi.org/10.1515/9783110264043
-
+
A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong].
EMAPA:16076
amnionic fold
@@ -432510,14 +432500,14 @@ https://doi.org/10.1515/9783110264043
amniotic fold
-
+
-
+
ISBN:0073040584
@@ -432712,7 +432702,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -432732,14 +432722,14 @@ https://doi.org/10.1515/9783110264043
atrium myocardial trabecula
-
+
-
+
ZFA
@@ -432791,7 +432781,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -432815,14 +432805,14 @@ https://doi.org/10.1515/9783110264043
atrioventricular septum
-
+
-
+
PMID:15797462
Wikipedia
@@ -432869,7 +432859,7 @@ https://doi.org/10.1515/9783110264043
-
+
The paired arteries that carry blood to the yolk sac from the dorsal aorta.
EHDAA2:0002208
EMAPA:16207
@@ -432881,14 +432871,14 @@ https://doi.org/10.1515/9783110264043
vitelline artery
http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png
-
+
-
+
ventral branch
@@ -433160,7 +433150,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -433191,14 +433181,14 @@ https://doi.org/10.1515/9783110264043
cervical region of vertebral column
-
+
-
+
FMA
@@ -433276,7 +433266,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -433310,14 +433300,14 @@ https://doi.org/10.1515/9783110264043
thoracic region of vertebral column
-
+
-
+
FMA
@@ -433498,7 +433488,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -433518,14 +433508,14 @@ https://doi.org/10.1515/9783110264043
subdivision of vertebral column
-
+
-
+
FMA
@@ -433607,7 +433597,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -433640,14 +433630,14 @@ https://doi.org/10.1515/9783110264043
aortico-pulmonary spiral septum
http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png
-
+
-
+
PMID:6844926
Wikipedia
@@ -433702,7 +433692,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -433746,14 +433736,14 @@ https://doi.org/10.1515/9783110264043
buccopharyngeal membrane
http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png
-
+
-
+
EHDAA2
@@ -433800,7 +433790,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -433841,14 +433831,14 @@ https://doi.org/10.1515/9783110264043
cloacal membrane
http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png
-
+
-
+
Wikipedia
@@ -433930,9 +433920,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
@@ -433949,34 +433939,34 @@ https://doi.org/10.1515/9783110264043
ethmoid bone primordium
-
+
-
+
-
+
-
+
FMA
-
+
AAO
-
+
EHDAA2
@@ -433997,7 +433987,7 @@ https://doi.org/10.1515/9783110264043
-
+
A differentiated genital tubercle that is part of a female reproductive system.
EHDAA:8118
EMAPA:18680
@@ -434009,14 +433999,14 @@ https://doi.org/10.1515/9783110264043
female genital tubercle
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -434238,8 +434228,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -434258,24 +434248,24 @@ https://doi.org/10.1515/9783110264043
future central tendon
-
+
-
+
-
+
EHDAA2
-
+
mesenchyme
cranial part
Wikipedia
@@ -434311,7 +434301,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -434335,14 +434325,14 @@ https://doi.org/10.1515/9783110264043
future spinal cord
-
+
-
+
EHDAA2
@@ -434388,8 +434378,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -434407,24 +434397,24 @@ https://doi.org/10.1515/9783110264043
gallbladder primordium
-
+
-
+
-
+
EMAPA
-
+
EHDAA2
@@ -434452,7 +434442,7 @@ https://doi.org/10.1515/9783110264043
-
+
A differentiated genital tubercle that is part of a male reproductive system.
EHDAA:8138
EMAPA:17969
@@ -434465,14 +434455,14 @@ https://doi.org/10.1515/9783110264043
male genital tubercle
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -434560,7 +434550,7 @@ https://doi.org/10.1515/9783110264043
-
+
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord.
TODO - check ordering; awaiting confirmation from JB
The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]
@@ -434575,7 +434565,7 @@ https://doi.org/10.1515/9783110264043
notochordal plate
-
+
@@ -434588,7 +434578,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -434625,7 +434615,7 @@ https://doi.org/10.1515/9783110264043
-
+
A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot.
EHDAA2:0001279
EHDAA:224
@@ -434642,14 +434632,14 @@ https://doi.org/10.1515/9783110264043
The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus.
notochordal process
-
+
-
+
EHDAA2
@@ -434728,7 +434718,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -434761,7 +434751,7 @@ https://doi.org/10.1515/9783110264043
pleuroperitoneal canal
-
+
@@ -434774,7 +434764,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -434806,8 +434796,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -434838,24 +434828,24 @@ https://doi.org/10.1515/9783110264043
The embryonic ventricle or primitive ventricle of the developing heart gives rise to the trabeculated parts of the left and right ventricles. In contrast, the smooth parts of the left and right ventricles originate from the embryological bulbus cordis. The primitive ventricle becomes divided by a septum, the septum inferius or ventricular septum, which grows upward from the lower part of the ventricle, its position being indicated on the surface of the heart by a furrow. Its dorsal part increases more rapidly than its ventral portion, and fuses with the dorsal part of the septum intermedium. For a time an interventricular foramen exists above its ventral portion, but this foramen is ultimately closed by the fusion of the aortic septum with the ventricular septum[WP]
future cardiac ventricle
-
+
-
+
-
+
ZFA
-
+
EMAPA
@@ -434905,8 +434895,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP].
check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme
UBERON:0009750
@@ -434923,11 +434913,11 @@ https://doi.org/10.1515/9783110264043
spleen primordium
-
+
-
+
@@ -434940,13 +434930,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2-modified
-
+
XAO
@@ -435011,7 +435001,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA:924
EMAPA:16663
RETIRED_EHDAA2:0002089
@@ -435023,14 +435013,14 @@ https://doi.org/10.1515/9783110264043
See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/13 and https://github.com/obophenotype/uberon/issues/693 -- consider merging into trigeminal ganglion, as this complicates the model
future trigeminal ganglion
-
+
-
+
EHDAA2
@@ -435371,7 +435361,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -435404,14 +435394,14 @@ https://doi.org/10.1515/9783110264043
os penis
-
+
-
+
Wikipedia
@@ -435465,7 +435455,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -435513,14 +435503,14 @@ https://doi.org/10.1515/9783110264043
os clitoris
-
+
-
+
Wikipedia
@@ -437157,7 +437147,7 @@ https://doi.org/10.1515/9783110264043
-
+
Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP].
BTO:0003117
EMAPA:19170
@@ -437176,14 +437166,14 @@ https://doi.org/10.1515/9783110264043
glans clitoris
http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif
-
+
-
+
cjm
@@ -437348,7 +437338,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -437361,7 +437351,7 @@ https://doi.org/10.1515/9783110264043
-
+
The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers.
In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]
EMAPA:17702
@@ -437379,24 +437369,24 @@ https://doi.org/10.1515/9783110264043
central tendon of diaphragm
-
+
-
+
-
+
VHOG
-
+
definitional
@@ -437935,7 +437925,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -437956,7 +437946,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0006815
areolar connective tissue
-
+
@@ -437969,7 +437959,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
@@ -438234,7 +438224,7 @@ https://doi.org/10.1515/9783110264043
-
+
A muscular coat that is part of a ureter.
EMAPA:28811
FMA:15893
@@ -438250,14 +438240,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0006855
muscular coat of ureter
-
+
-
+
FMA
@@ -438548,7 +438538,7 @@ https://doi.org/10.1515/9783110264043
-
+
A head mesenchyme that develops_from a mesoderm.
merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme
AAO:0011051
@@ -438576,7 +438566,7 @@ https://doi.org/10.1515/9783110264043
head mesenchyme from mesoderm
-
+
@@ -438589,7 +438579,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
XAO
@@ -439299,7 +439289,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -439345,14 +439335,14 @@ https://doi.org/10.1515/9783110264043
efferent duct
http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg
-
+
-
+
FMA
@@ -439418,7 +439408,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -439446,14 +439436,14 @@ https://doi.org/10.1515/9783110264043
male genital duct
https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb
-
+
-
+
FMA-abduced-lr
@@ -439634,7 +439624,7 @@ https://doi.org/10.1515/9783110264043
-
+
The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis.
CALOHA:TS-1246
@@ -439656,14 +439646,14 @@ https://doi.org/10.1515/9783110264043
ovary stroma
-
+
-
+
FMA
@@ -440260,7 +440250,7 @@ https://doi.org/10.1515/9783110264043
-
+
Cranial neural crest that migrates into the mandibular arch.
TAO:0007064
XAO:0000024
@@ -440269,7 +440259,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0007098
mandibular neural crest
-
+
@@ -440282,7 +440272,7 @@ https://doi.org/10.1515/9783110264043
-
+
ZFA
@@ -440301,7 +440291,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -440312,7 +440302,7 @@ https://doi.org/10.1515/9783110264043
-
+
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
SPD:0000130
@@ -440327,14 +440317,14 @@ https://doi.org/10.1515/9783110264043
Gene notes: Bmp, Nkx, Gata
primary circulatory organ
-
+
-
+
GO uses blood circulation generically to include the haemolymphatic fluid of arthropods
@@ -440369,8 +440359,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta.
The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively
The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present.
@@ -440398,24 +440388,24 @@ https://doi.org/10.1515/9783110264043
chorionic villus
http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png
-
+
-
+
-
+
BTO
-
+
MP-def
@@ -441475,7 +441465,7 @@ https://doi.org/10.1515/9783110264043
-
+
relationship to Meckel's cartilage to be added
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
EHDAA2:0000031
@@ -441489,14 +441479,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007237
1st arch mandibular component
-
+
-
+
EHDAA2
@@ -441534,7 +441524,7 @@ https://doi.org/10.1515/9783110264043
-
+
relationship to palatoquadrate to be added
Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]
EHDAA2:0000038
@@ -441545,14 +441535,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007238
1st arch maxillary component
-
+
-
+
EHDAA2
@@ -441650,7 +441640,7 @@ https://doi.org/10.1515/9783110264043
-
+
A tunica adventitia that is part of a artery.
EMAPA:36295
EV:0100030
@@ -441662,14 +441652,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007240
tunica adventitia of artery
-
+
-
+
FMA
@@ -442115,7 +442105,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -442136,14 +442126,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007272
pectoral appendage skeleton
-
+
-
+
VSAO
@@ -442178,7 +442168,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -442196,14 +442186,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007273
pelvic appendage skeleton
-
+
-
+
VSAO
@@ -442236,8 +442226,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -442264,24 +442254,24 @@ https://doi.org/10.1515/9783110264043
presumptive hindbrain
-
+
-
+
-
+
XAO-abduced
-
+
cjm
@@ -442338,7 +442328,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -442352,14 +442342,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007278
presumptive sinus venosus
-
+
-
+
ZFA
@@ -442445,7 +442435,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -442464,14 +442454,14 @@ https://doi.org/10.1515/9783110264043
presumptive midbrain hindbrain boundary
-
+
-
+
ZFA
@@ -442510,7 +442500,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -442527,14 +442517,14 @@ https://doi.org/10.1515/9783110264043
presumptive segmental plate
-
+
-
+
https://github.com/obophenotype/uberon/wiki/The-neural-crest
EDHAA2
@@ -442633,7 +442623,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -442659,7 +442649,7 @@ https://doi.org/10.1515/9783110264043
presumptive paraxial mesoderm
-
+
@@ -442675,7 +442665,7 @@ https://doi.org/10.1515/9783110264043
-
+
https://github.com/obophenotype/uberon/issues/1277
@@ -443069,7 +443059,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -443115,7 +443105,7 @@ https://doi.org/10.1515/9783110264043
pancreatic duct
http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png
-
+
@@ -443128,7 +443118,7 @@ https://doi.org/10.1515/9783110264043
-
+
MA
@@ -443269,7 +443259,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -443296,14 +443286,14 @@ https://doi.org/10.1515/9783110264043
outer epithelium
-
+
-
+
Wikipedia:Epidermis_(zoology)
@@ -443834,7 +443824,7 @@ https://doi.org/10.1515/9783110264043
-
+
A collection of connected epithelial tubes with a single portal.
AEO:0000117
EHDAA2:0003117
@@ -443843,7 +443833,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0007501
arborizing epithelial duct system
-
+
@@ -443856,7 +443846,7 @@ https://doi.org/10.1515/9783110264043
-
+
AEO
@@ -443992,7 +443982,7 @@ https://doi.org/10.1515/9783110264043
-
+
Mesenchyme with little extracellular matrix.
AEO:0000146
EHDAA2:0003146
@@ -444000,7 +443990,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0007524
dense mesenchyme tissue
-
+
@@ -444013,7 +444003,7 @@ https://doi.org/10.1515/9783110264043
-
+
AEO
@@ -444258,7 +444248,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -444278,14 +444268,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007616
layer of synovial tissue
-
+
-
+
BTO
@@ -444498,7 +444488,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -444524,7 +444514,7 @@ https://doi.org/10.1515/9783110264043
trigeminal nuclear complex
http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png
-
+
@@ -444537,7 +444527,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
@@ -444786,7 +444776,7 @@ https://doi.org/10.1515/9783110264043
-
+
EFO:0003626
EHDAA2:0001457
EHDAA:962
@@ -444805,14 +444795,14 @@ https://doi.org/10.1515/9783110264043
early pharyngeal endoderm
http://dev.biologists.org/content/128/22/4573.full
-
+
-
+
cjm
@@ -444950,26 +444940,26 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
An endothelium that is part of a umbilical artery.
BTO:0000857
uberon
UBERON:0007778
umbilical artery endothelium
-
+
-
+
BTO
@@ -445099,7 +445089,7 @@ https://doi.org/10.1515/9783110264043
-
+
Anatomical system that consists of all blood and lymph vessels.
consider merging with vasculature
@@ -445118,14 +445108,14 @@ https://doi.org/10.1515/9783110264043
vascular system
-
+
-
+
MA
@@ -445159,7 +445149,7 @@ https://doi.org/10.1515/9783110264043
-
+
A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord.
TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels
BTO:0004705
@@ -445169,7 +445159,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0007806
connecting stalk
-
+
@@ -445182,7 +445172,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -445221,7 +445211,7 @@ https://doi.org/10.1515/9783110264043
-
+
A vasculature that is part of a connecting stalk.
EHDAA2:0000313
connecting stalk blood vessels
@@ -445231,14 +445221,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007807
connecting stalk vasculature
-
+
-
+
EHDAA2
@@ -445430,7 +445420,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -445488,14 +445478,14 @@ https://doi.org/10.1515/9783110264043
post-anal tail
-
+
-
+
possible exception in hemichordates
cjm
@@ -445660,7 +445650,7 @@ https://doi.org/10.1515/9783110264043
-
+
Mesentery that is located in the peritoneum.
FMA:20570
TAO:0005129
@@ -445670,14 +445660,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0007826
peritoneal mesentery
-
+
-
+
FMA
@@ -446044,7 +446034,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -446087,14 +446077,14 @@ https://doi.org/10.1515/9783110264043
pelvic girdle skeleton
http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png
-
+
-
+
PMID:21455939
@@ -446258,8 +446248,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -446285,11 +446275,11 @@ https://doi.org/10.1515/9783110264043
cartilage element
-
+
-
+
@@ -446302,13 +446292,13 @@ https://doi.org/10.1515/9783110264043
-
+
VSAO
-
+
VSAO
@@ -446517,12 +446507,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
A bone that is part of a craniocervical region.
EMAPA:37245
MA:0000569
@@ -446532,7 +446522,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0007914
bone of craniocervical region
-
+
@@ -446545,7 +446535,7 @@ https://doi.org/10.1515/9783110264043
-
+
MA
@@ -446924,12 +446914,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
Musculature system of the pharyngeal and head regions.
in MA this is restricted to skeletal muscles
EMAPA:37259
@@ -446943,7 +446933,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0008229
craniocervical region musculature
-
+
@@ -446956,7 +446946,7 @@ https://doi.org/10.1515/9783110264043
-
+
MA
@@ -447003,8 +446993,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax.
EMAPA:37234
FMA:24217
@@ -447020,25 +447010,25 @@ https://doi.org/10.1515/9783110264043
UBERON:0008231
dorsal thoracic segment of trunk
-
+
-
+
-
+
FMA
MA
-
+
FMA
@@ -447099,13 +447089,13 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
A muscle of back that is part of a dorsal thoracic segment of trunk.
EMAPA:37261
MA:0000508
@@ -447114,7 +447104,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0008243
upper back muscle
-
+
@@ -447127,7 +447117,7 @@ https://doi.org/10.1515/9783110264043
-
+
MA
@@ -447340,7 +447330,7 @@ https://doi.org/10.1515/9783110264043
-
+
An epithelium that is part of a duodenum.
CALOHA:TS-2087
@@ -447354,14 +447344,14 @@ https://doi.org/10.1515/9783110264043
duodenal epithelium
-
+
-
+
FMA
@@ -447462,7 +447452,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -447473,7 +447463,7 @@ https://doi.org/10.1515/9783110264043
-
+
An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers.
EHDAA2:0000444
EHDAA:42
@@ -447489,14 +447479,14 @@ https://doi.org/10.1515/9783110264043
The epiblast cells (appearing on day 8 of human embryonic development) make up a columnar epithelium with dense microvilli on the apical surface. During gastrulation, the epiblast cells undergo epithelial-to-mesenchymal transition and delaminate to become the loose mesenchyme of the primitive streak. The epiblast is present in postimplantation mouse embryos between E5.5-E7.5.
inner cell mass derived epiblast
-
+
-
+
Wikipedia
@@ -447713,7 +447703,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -447728,7 +447718,7 @@ https://doi.org/10.1515/9783110264043
neural tube derived brain
https://github.com/obophenotype/uberon/issues/338
-
+
@@ -447741,7 +447731,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
@@ -447770,7 +447760,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -447790,14 +447780,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0008824
duct of epididymis
-
+
-
+
FMA
@@ -447835,8 +447825,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts.
in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10
The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut.
@@ -447855,11 +447845,11 @@ https://doi.org/10.1515/9783110264043
hepatic diverticulum
http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png
-
+
-
+
@@ -447872,14 +447862,14 @@ https://doi.org/10.1515/9783110264043
-
+
caudal part
EHDAA2
-
+
EHDAA2
@@ -447918,13 +447908,13 @@ https://doi.org/10.1515/9783110264043
-
+
BTO:0001642
uberon
UBERON:0008836
liver bud
-
+
@@ -447937,7 +447927,7 @@ https://doi.org/10.1515/9783110264043
-
+
http://www.stembook.org/node/512
@@ -447954,7 +447944,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -447966,10 +447956,10 @@ https://doi.org/10.1515/9783110264043
-
+
+
+
-
-
Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified].
logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71
Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]
@@ -447994,44 +447984,44 @@ https://doi.org/10.1515/9783110264043
skeletal ligament
https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg
-
+
-
+
-
+
-
+
-
+
AEO
-
+
AEO
-
+
bones or cartilage organs
-
+
VSAO
@@ -448160,7 +448150,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -448187,14 +448177,14 @@ https://doi.org/10.1515/9783110264043
stomach muscularis externa
-
+
-
+
MA-abduced
@@ -448240,7 +448230,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -448272,7 +448262,7 @@ https://doi.org/10.1515/9783110264043
pyloric canal
https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg
-
+
@@ -448285,7 +448275,7 @@ https://doi.org/10.1515/9783110264043
-
+
Wikipedia
@@ -448339,7 +448329,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -448364,7 +448354,7 @@ https://doi.org/10.1515/9783110264043
pyloric gastric gland
http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png
-
+
@@ -448377,7 +448367,7 @@ https://doi.org/10.1515/9783110264043
-
+
Wikipedia:Tubular_gland
@@ -448437,7 +448427,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -448470,14 +448460,14 @@ https://doi.org/10.1515/9783110264043
hypodermis skeletal muscle layer
-
+
-
+
MP-def
@@ -448659,8 +448649,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
Subdivision of endoskeleton derived from pharyngeal arches.
@@ -448693,24 +448683,24 @@ https://doi.org/10.1515/9783110264043
splanchnocranium
http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg
-
+
-
+
-
+
https://github.com/obophenotype/uberon/issues/83
-
+
redundant
Grays
PMID:11237469
@@ -448828,13 +448818,13 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO].
Intramembranous bone that forms superficially in the organism.[TAO]
other AOs are not yet in sync with this classification
@@ -448849,7 +448839,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0008907
dermal bone
-
+
@@ -448868,7 +448858,7 @@ https://doi.org/10.1515/9783110264043
-
+
VSAO
@@ -448980,13 +448970,13 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
A parenchyma that is part of a lung.
EMAPA:35522
FMA:27360
@@ -448999,7 +448989,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0008946
lung parenchyma
-
+
@@ -449012,7 +449002,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
@@ -449141,12 +449131,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
The functional tissue of the kidney, consisting of the nephrons.
BTO:0003604
FMA:15574
@@ -449157,7 +449147,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0008987
renal parenchyma
-
+
@@ -449170,7 +449160,7 @@ https://doi.org/10.1515/9783110264043
-
+
FMA
@@ -449837,13 +449827,13 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
Cranial ganglion which develops from an epibranchial placode.
BTO:0006250
TAO:0001555
@@ -449854,7 +449844,7 @@ https://doi.org/10.1515/9783110264043
Epibranchial ganglia orchestrate the development of the cranial neurogenic crest
epibranchial ganglion
-
+
@@ -449867,7 +449857,7 @@ https://doi.org/10.1515/9783110264043
-
+
NCBIBook:NBK53175
@@ -449919,8 +449909,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
Endocardium that is part of the right atrium.
EHDAA2:0000274
FMA:7281
@@ -449934,24 +449924,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0009129
right atrium endocardium
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -450115,7 +450105,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -450132,14 +450122,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009142
entire embryonic mesenchyme
-
+
-
+
EHDAA2
@@ -450155,7 +450145,7 @@ https://doi.org/10.1515/9783110264043
-
+
EMAPA:16549
RETIRED_EHDAA2:0001454
pharyngeal region
@@ -450163,14 +450153,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009145
pharyngeal region of foregut
-
+
-
+
EHDAA2
@@ -450207,8 +450197,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -450222,11 +450212,11 @@ https://doi.org/10.1515/9783110264043
UBERON:0009191
sphenoid bone pre-cartilage condensation
-
+
-
+
@@ -450245,13 +450235,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
EHDAA2
@@ -450386,12 +450376,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
Mesenchyme that is part of a medial nasal prominence.
EHDAA2:0001077
EMAPA:16810
@@ -450400,14 +450390,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009204
medial nasal process mesenchyme
-
+
-
+
EHDAA2
@@ -450642,7 +450632,7 @@ https://doi.org/10.1515/9783110264043
-
+
A portion of mesenchymal tissue associated with an individual pharyngeal arch.
this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures.
EMAPA:32755
@@ -450654,7 +450644,7 @@ https://doi.org/10.1515/9783110264043
pharyngeal arch mesenchymal region
-
+
@@ -450667,7 +450657,7 @@ https://doi.org/10.1515/9783110264043
-
+
cjm
@@ -450714,14 +450704,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
An epithelium that is part of a foregut-midgut junction.
EHDAA2:0000573
EMAPA:16564
@@ -450730,24 +450720,24 @@ https://doi.org/10.1515/9783110264043
epithelium of foregut-midgut junction
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -451196,7 +451186,7 @@ https://doi.org/10.1515/9783110264043
-
+
A submucosa that is part of a intestine.
FMA:15696
submucosa of intestine
@@ -451204,14 +451194,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009566
intestinal submucosa
-
+
-
+
FMA
@@ -451424,7 +451414,7 @@ https://doi.org/10.1515/9783110264043
-
+
A sulcus limitans of neural tube that is part of a future medulla oblongata.
EHDAA2:0001100
EMAPA:17561
@@ -451432,14 +451422,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009576
medulla oblongata sulcus limitans
-
+
-
+
EHDAA2
@@ -451615,12 +451605,12 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
Mesenchyme that is part of a 1st arch mandibular component.
UBERON:0010043
EHDAA2:0000034
@@ -451633,14 +451623,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009584
1st arch mandibular mesenchyme
-
+
-
+
EMAPA
@@ -451756,9 +451746,9 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
@@ -451772,7 +451762,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0009611
midbrain neural plate
-
+
@@ -451781,20 +451771,20 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
ZFA
-
+
ZFA
@@ -451809,9 +451799,9 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
@@ -451825,7 +451815,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0009614
hindbrain neural plate
-
+
@@ -451834,20 +451824,20 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
ZFA
-
+
ZFA
@@ -451863,14 +451853,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
TODO - developmental relationships for lines
TAO:0007044
ZFA:0007044
@@ -451880,24 +451870,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0009615
midbrain hindbrain boundary neural plate
-
+
-
+
-
+
ZFA
-
+
https://github.com/obophenotype/uberon/issues/438
Bgee:AN
@@ -451931,14 +451921,14 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
@@ -451963,24 +451953,24 @@ https://doi.org/10.1515/9783110264043
presumptive midbrain
-
+
-
+
-
+
ZFA
-
+
ZFA
@@ -452026,7 +452016,7 @@ https://doi.org/10.1515/9783110264043
-
+
Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles.
A major contributor to neurocranium [PMID:16313393]
EHDAA2:0000736
@@ -452043,14 +452033,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009617
head paraxial mesoderm
-
+
-
+
EHDAA2
@@ -452103,7 +452093,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2:0002094
trunk and cervical paraxial mesenchyme
uberon
@@ -452111,14 +452101,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009618
trunk paraxial mesoderm
-
+
-
+
EHDAA2
@@ -452189,7 +452179,7 @@ https://doi.org/10.1515/9783110264043
-
+
A basement membrane that is part of a nephron tubule.
EMAPA:37490
MA:0001680
@@ -452203,14 +452193,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009651
nephron tubule basement membrane
-
+
-
+
true
https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships
@@ -452383,7 +452373,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2:0004566
EMAPA:32911
MA:0003203
@@ -452394,14 +452384,14 @@ https://doi.org/10.1515/9783110264043
gut mesentery
https://github.com/obophenotype/uberon/issues/509
-
+
-
+
EHDAA2
@@ -452488,8 +452478,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -452506,24 +452496,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0009670
rectal lumen
-
+
-
+
-
+
cjm
-
+
EHDAA2
@@ -452547,9 +452537,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
EHDAA2:0001371
uberon
@@ -452559,15 +452549,15 @@ https://doi.org/10.1515/9783110264043
dorsal pancreas
-
+
-
+
-
+
@@ -452580,19 +452570,19 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
EHDAA2
-
+
cjm
@@ -452604,9 +452594,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
EHDAA2:0001393
uberon
@@ -452616,15 +452606,15 @@ https://doi.org/10.1515/9783110264043
ventral pancreas
-
+
-
+
-
+
@@ -452637,19 +452627,19 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
EHDAA2
-
+
cjm
@@ -452676,8 +452666,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
Any endocardium that is part of the right ventricle of the heart.
Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk.
EHDAA2:0002188
@@ -452694,24 +452684,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0009712
endocardium of right ventricle
-
+
-
+
-
+
EHDAA2
-
+
FMA
@@ -452774,7 +452764,7 @@ https://doi.org/10.1515/9783110264043
-
+
Any endocardium that is part of the left ventricle of the heart.
Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta.
EHDAA2:0002182
@@ -452790,14 +452780,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009713
endocardium of left ventricle
-
+
-
+
FMA
@@ -452889,7 +452879,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -452904,14 +452894,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009722
entire pharyngeal arch endoderm
-
+
-
+
EHDAA2
@@ -453114,7 +453104,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -453127,7 +453117,7 @@ https://doi.org/10.1515/9783110264043
-
+
A serous sac that has the pleura and the pleural cavity as parts.
despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac
EHDAA2:0004737
@@ -453138,24 +453128,24 @@ https://doi.org/10.1515/9783110264043
pleural sac
-
+
-
+
-
+
FMA
-
+
FMA-abduced-lr
@@ -453268,7 +453258,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -453287,14 +453277,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0009844
urogenital sinus lumen
-
+
-
+
EHDAA2
@@ -453309,7 +453299,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -453325,7 +453315,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0009845
urogenital sinus mesenchyme
-
+
@@ -453337,7 +453327,7 @@ https://doi.org/10.1515/9783110264043
-
+
PMID:18977204
@@ -453379,8 +453369,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
An epithelium that is part of a embryonic cloaca.
cloacal epithelium
EHDAA2:0004585
@@ -453388,24 +453378,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0009846
embryonic cloacal epithelium
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -453638,7 +453628,7 @@ https://doi.org/10.1515/9783110264043
-
+
EFO:0003704
TAO:0005041
ZFA:0005041
@@ -453648,14 +453638,14 @@ https://doi.org/10.1515/9783110264043
anterior lateral plate mesoderm
-
+
-
+
ZFA
@@ -453671,7 +453661,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -453701,7 +453691,7 @@ https://doi.org/10.1515/9783110264043
medullary ray
-
+
@@ -453714,7 +453704,7 @@ https://doi.org/10.1515/9783110264043
-
+
MP
@@ -453968,9 +453958,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
@@ -453990,34 +453980,34 @@ https://doi.org/10.1515/9783110264043
UBERON:0009889
secondary heart field
-
+
-
+
-
+
-
+
GO:0003129
-
+
PMID:17276708
-
+
PMID:17276708
@@ -454288,7 +454278,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -454327,14 +454317,14 @@ https://doi.org/10.1515/9783110264043
Alternate definition: One of the subdivisions of the kidney, consisting of a medullary ray and that portion of the convoluted port (renal corpuscles and convoluted tubules) associated with its collecting duct. -http://www.mondofacto.com/facts/dictionary?lobulus+corticalis+renalis
renal lobule
-
+
-
+
FMA
@@ -454524,14 +454514,14 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2:0001315
EHDAA:1122
uberon
UBERON:0009920
optic neural crest
-
+
@@ -454544,7 +454534,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -454718,10 +454708,10 @@ https://doi.org/10.1515/9783110264043
-
+
-
-
+
+
@@ -454741,7 +454731,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0009958
bladder lumen
-
+
@@ -454750,30 +454740,30 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
-
+
FMA
-
+
FMA
-
+
EHDAA2
@@ -454883,7 +454873,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -454915,14 +454905,14 @@ https://doi.org/10.1515/9783110264043
ureteropelvic junction
-
+
-
+
MP
@@ -454966,7 +454956,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -454999,14 +454989,14 @@ https://doi.org/10.1515/9783110264043
ureterovesical junction
-
+
-
+
MP
@@ -455318,8 +455308,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells.
EHDAA2:0001459
EMAPA:16550
@@ -455331,11 +455321,11 @@ https://doi.org/10.1515/9783110264043
UBERON:0010046
entire pharyngeal arch associated mesenchyme
-
+
-
+
@@ -455348,13 +455338,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
cjm
@@ -455535,9 +455525,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
@@ -455551,34 +455541,34 @@ https://doi.org/10.1515/9783110264043
UBERON:0010083
future dermis
-
+
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
-
+
XAO
@@ -455605,9 +455595,9 @@ https://doi.org/10.1515/9783110264043
-
-
-
+
+
+
@@ -455620,34 +455610,34 @@ https://doi.org/10.1515/9783110264043
UBERON:0010084
future diaphragm
-
+
-
+
-
+
-
+
EHDAA2
-
+
PMID:23586979
-
+
PMID:23586979
@@ -455834,7 +455824,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -455843,7 +455833,7 @@ https://doi.org/10.1515/9783110264043
-
+
A sex cord that is part of a indifferent gonad.
note that this represents the indifferent structure.
EHDAA2:0004051
@@ -455853,7 +455843,7 @@ https://doi.org/10.1515/9783110264043
UBERON:0010141
primitive sex cord of indifferent gonad
-
+
@@ -455862,20 +455852,20 @@ https://doi.org/10.1515/9783110264043
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -456086,7 +456076,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456104,14 +456094,14 @@ https://doi.org/10.1515/9783110264043
post-anal tail tip
-
+
-
+
MA
@@ -456387,7 +456377,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456404,7 +456394,7 @@ https://doi.org/10.1515/9783110264043
pair of dorsal aortae
-
+
@@ -456417,7 +456407,7 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
@@ -456440,7 +456430,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456452,14 +456442,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0010191
aortic system
-
+
-
+
Wikipedia
@@ -456642,7 +456632,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456660,14 +456650,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0010227
future cardiac atrium
-
+
-
+
ZFA
@@ -456702,7 +456692,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456727,14 +456717,14 @@ https://doi.org/10.1515/9783110264043
eyeball of camera-type eye
-
+
-
+
FMA
@@ -456820,7 +456810,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456830,8 +456820,8 @@ https://doi.org/10.1515/9783110264043
-
-
+
+
@@ -456844,11 +456834,11 @@ https://doi.org/10.1515/9783110264043
UBERON:0010252
1st arch mandibular mesenchyme from neural crest
-
+
-
+
@@ -456861,13 +456851,13 @@ https://doi.org/10.1515/9783110264043
-
+
EHDAA2
-
+
EHDAA2
@@ -456886,7 +456876,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456896,32 +456886,32 @@ https://doi.org/10.1515/9783110264043
+
-
Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme.
EHDAA2:0000044
uberon
UBERON:0010253
1st arch maxillary mesenchyme from neural crest
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -456940,7 +456930,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -456951,8 +456941,8 @@ https://doi.org/10.1515/9783110264043
+
-
Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme.
In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]
EHDAA2:0000098
@@ -456967,24 +456957,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0010256
4th arch mesenchyme from neural crest
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -457025,7 +457015,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -457036,8 +457026,8 @@ https://doi.org/10.1515/9783110264043
+
-
Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme.
EHDAA2:0004077
neural crest derived arch 6 mesenchyme
@@ -457047,24 +457037,24 @@ https://doi.org/10.1515/9783110264043
UBERON:0010257
6th arch mesenchyme from neural crest
-
+
-
+
-
+
EHDAA2
-
+
EHDAA2
@@ -457091,7 +457081,7 @@ https://doi.org/10.1515/9783110264043
-
+
@@ -457104,14 +457094,14 @@ https://doi.org/10.1515/9783110264043
UBERON:0010258
mesenchyme from rhombencephalic neural crest
-
+