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Merge pull request #6 from brain-bican/wmbo_inconsistencies
Wmbo inconsistencies resolution
2 parents 76c98f5 + 4f5a481 commit 01d70be

19 files changed

+8592
-6346
lines changed

‎mbao-base.json‎

Lines changed: 108 additions & 126 deletions
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‎mbao-base.obo‎

Lines changed: 66 additions & 51 deletions
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@@ -1,12 +1,12 @@
11
format-version: 1.2
2-
data-version: https://purl.brain-bican.org/ontology/mbao/releases/2025-04-17/mbao-base.owl
2+
data-version: https://purl.brain-bican.org/ontology/mbao/releases/2025-07-04/mbao-base.owl
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ontology: https://purl.brain-bican.org/ontology/mbao/mbao-base.owl
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property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
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property_value: http://purl.org/dc/terms/description "An application ontology built by combining ontologised versions of the Allen Institute Mouse Brain Atlas (MBA) StructureGraph mapped to Uberon." xsd:string
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property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/
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property_value: http://purl.org/dc/terms/title "Mouse Brain Atlas Ontology" xsd:string
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property_value: IAO:0000700 MBA:997
9-
property_value: owl:versionInfo "2025-04-17" xsd:string
9+
property_value: owl:versionInfo "2025-07-04" xsd:string
1010

1111
[Term]
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id: CL:0000000
@@ -260,14 +260,6 @@ property_value: prefLabel "photoreceptor cell" xsd:string
260260
id: CL:0000211
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property_value: prefLabel "electrically active cell" xsd:string
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263-
[Term]
264-
id: CL:0000213
265-
property_value: prefLabel "lining cell" xsd:string
266-
267-
[Term]
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id: CL:0000215
269-
property_value: prefLabel "barrier cell" xsd:string
270-
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[Term]
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id: CL:0000219
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property_value: prefLabel "motile cell" xsd:string
@@ -924,6 +916,14 @@ property_value: prefLabel "organelle lumen" xsd:string
924916
id: GO:0043292
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property_value: prefLabel "contractile muscle fiber" xsd:string
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919+
[Term]
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id: GO:0044292
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property_value: prefLabel "dendrite terminus" xsd:string
922+
923+
[Term]
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id: GO:0044293
925+
property_value: prefLabel "dendriole" xsd:string
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[Term]
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id: GO:0044297
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property_value: prefLabel "cell body" xsd:string
@@ -16456,8 +16456,8 @@ synonym: "XIn" EXACT []
1645616456
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=717
1645716457
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=717
1645816458
xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=717
16459-
is_a: UBERON:0002019
16460-
intersection_of: UBERON:0002019
16459+
is_a: UBERON:0014615
16460+
intersection_of: UBERON:0014615
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intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1646216462
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
1646316463
relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -16877,11 +16877,9 @@ synonym: "DGcr-mo" EXACT []
1687716877
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=742
1687816878
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=742
1687916879
xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=742
16880-
is_a: UBERON:0004679
16881-
intersection_of: UBERON:0004679
16882-
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1688316880
relationship: BFO:0000050 MBA:734 ! part of Dentate gyrus crest
1688416881
relationship: BFO:0000050 NCBITaxon:10090 ! part of
16882+
relationship: BFO:0000050 UBERON:0004679 ! part of
1688516883
property_value: IAO:0000028 "DGcr-mo" xsd:string
1688616884
property_value: IAO:0000589 "dentate gyrus crest, molecular layer" xsd:string
1688716885
property_value: prefLabel "Dentate gyrus crest, molecular layer ( mouse )" xsd:string
@@ -17139,11 +17137,9 @@ synonym: "DGcr-sg" EXACT []
1713917137
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=758
1714017138
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=758
1714117139
xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=758
17142-
is_a: UBERON:0005381
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intersection_of: UBERON:0005381
17144-
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1714517140
relationship: BFO:0000050 MBA:734 ! part of Dentate gyrus crest
1714617141
relationship: BFO:0000050 NCBITaxon:10090 ! part of
17142+
relationship: BFO:0000050 UBERON:0005381 ! part of
1714717143
property_value: IAO:0000028 "DGcr-sg" xsd:string
1714817144
property_value: IAO:0000589 "dentate gyrus crest, granule cell layer" xsd:string
1714917145
property_value: prefLabel "Dentate gyrus crest, granule cell layer ( mouse )" xsd:string
@@ -17647,11 +17643,9 @@ synonym: "DGlb-sg" EXACT []
1764717643
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=790
1764817644
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=790
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=790
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is_a: UBERON:0005381
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intersection_of: UBERON:0005381
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intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1765317646
relationship: BFO:0000050 MBA:766 ! part of Dentate gyrus lateral blade
1765417647
relationship: BFO:0000050 NCBITaxon:10090 ! part of
17648+
relationship: BFO:0000050 UBERON:0005381 ! part of
1765517649
property_value: IAO:0000028 "DGlb-sg" xsd:string
1765617650
property_value: IAO:0000589 "dentate gyrus lateral blade, granule cell layer" xsd:string
1765717651
property_value: prefLabel "Dentate gyrus lateral blade, granule cell layer ( mouse )" xsd:string
@@ -17773,8 +17767,8 @@ synonym: "VIIn" EXACT []
1777317767
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=798
1777417768
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=798
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=798
17776-
is_a: UBERON:0001647
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intersection_of: UBERON:0001647
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is_a: UBERON:0004674
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intersection_of: UBERON:0004674
1777817772
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1777917773
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -17805,8 +17799,8 @@ synonym: "grey" EXACT []
1780517799
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=8
1780617800
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=8
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=8
17808-
is_a: UBERON:0000955
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intersection_of: UBERON:0000955
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is_a: UBERON:0002616
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intersection_of: UBERON:0002616
1781017804
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1781117805
relationship: BFO:0000050 MBA:997 ! part of brain
1781217806
relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -17953,8 +17947,8 @@ synonym: "IXn" EXACT []
1795317947
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=808
1795417948
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=808
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=808
17956-
is_a: UBERON:0001649
17957-
intersection_of: UBERON:0001649
17950+
is_a: UBERON:0019310
17951+
intersection_of: UBERON:0019310
1795817952
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1795917953
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -18047,8 +18041,8 @@ synonym: "XIIn" EXACT []
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xref: http://atlas.brain-map.org/atlas?atlas=1#structure=813
1804818042
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=813
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=813
18050-
is_a: UBERON:0001650
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intersection_of: UBERON:0001650
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is_a: UBERON:0004675
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intersection_of: UBERON:0004675
1805218046
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1805318047
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -18218,11 +18212,9 @@ synonym: "DGmb-sg" EXACT []
1821818212
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=823
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xref: http://atlas.brain-map.org/atlas?atlas=2#structure=823
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=823
18221-
is_a: UBERON:0005381
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intersection_of: UBERON:0005381
18223-
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1822418215
relationship: BFO:0000050 MBA:799 ! part of Dentate gyrus medial blade
1822518216
relationship: BFO:0000050 NCBITaxon:10090 ! part of
18217+
relationship: BFO:0000050 UBERON:0005381 ! part of
1822618218
property_value: IAO:0000028 "DGmb-sg" xsd:string
1822718219
property_value: IAO:0000589 "dentate gyrus medial blade, granule cell layer" xsd:string
1822818220
property_value: prefLabel "Dentate gyrus medial blade, granule cell layer ( mouse )" xsd:string
@@ -18377,8 +18369,8 @@ synonym: "IIIn" EXACT []
1837718369
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=832
1837818370
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=832
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=832
18380-
is_a: UBERON:0001643
18381-
intersection_of: UBERON:0001643
18372+
is_a: UBERON:0002668
18373+
intersection_of: UBERON:0002668
1838218374
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1838318375
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
1838418376
relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -18525,8 +18517,8 @@ synonym: "In" EXACT []
1852518517
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=840
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xref: http://atlas.brain-map.org/atlas?atlas=2#structure=840
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=840
18528-
is_a: UBERON:0001579
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intersection_of: UBERON:0001579
18520+
is_a: UBERON:0019311
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intersection_of: UBERON:0019311
1853018522
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
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relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -19569,8 +19561,8 @@ synonym: "Vn" EXACT []
1956919561
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=901
1957019562
xref: http://atlas.brain-map.org/atlas?atlas=2#structure=901
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=901
19572-
is_a: UBERON:0001645
19573-
intersection_of: UBERON:0001645
19564+
is_a: UBERON:0004673
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intersection_of: UBERON:0004673
1957419566
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
1957519567
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -19838,8 +19830,8 @@ synonym: "Xn" EXACT []
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xref: http://atlas.brain-map.org/atlas?atlas=1#structure=917
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xref: http://atlas.brain-map.org/atlas?atlas=2#structure=917
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=917
19841-
is_a: UBERON:0001759
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intersection_of: UBERON:0001759
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is_a: UBERON:0011213
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intersection_of: UBERON:0011213
1984319835
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
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relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -20112,8 +20104,8 @@ synonym: "VIIIn" EXACT []
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xref: http://atlas.brain-map.org/atlas?atlas=1#structure=933
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xref: http://atlas.brain-map.org/atlas?atlas=2#structure=933
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=933
20115-
is_a: UBERON:0001648
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intersection_of: UBERON:0001648
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is_a: UBERON:0002731
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intersection_of: UBERON:0002731
2011720109
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
2011820110
relationship: BFO:0000050 MBA:967 ! part of cranial nerves
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -20340,6 +20332,7 @@ intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
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relationship: BFO:0000050 MBA:467 ! part of Hypothalamic medial zone
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
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property_value: IAO:0000028 "PH" xsd:string
20335+
property_value: IAO:0000589 "posterior hyfpothalamic nucleus" xsd:string
2034320336
property_value: IAO:0000589 "posterior hypothalamic nucleus" xsd:string
2034420337
property_value: prefLabel "Posterior hypothalamic nucleus ( mouse )" xsd:string
2034520338
property_value: status "Verified" xsd:string {source="https://ror.org/03cpe7c52"}
@@ -20369,11 +20362,9 @@ synonym: "cVIIIn" EXACT []
2036920362
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=948
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xref: http://atlas.brain-map.org/atlas?atlas=2#structure=948
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=948
20372-
is_a: UBERON:0004727
20373-
intersection_of: UBERON:0004727
20374-
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
2037520365
relationship: BFO:0000050 MBA:933 ! part of vestibulocochlear nerve
2037620366
relationship: BFO:0000050 NCBITaxon:10090 ! part of
20367+
relationship: BFO:0000050 UBERON:0002731 ! part of
2037720368
property_value: IAO:0000028 "cVIIIn" xsd:string
2037820369
property_value: IAO:0000589 "cochlear nerve" xsd:string
2037920370
property_value: prefLabel "cochlear nerve ( mouse )" xsd:string
@@ -20690,8 +20681,8 @@ synonym: "cm" EXACT []
2069020681
xref: http://atlas.brain-map.org/atlas?atlas=1#structure=967
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xref: http://atlas.brain-map.org/atlas?atlas=2#structure=967
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xref: http://atlas.brain-map.org/atlas?atlas=602630314#structure=967
20693-
is_a: UBERON:0001785
20694-
intersection_of: UBERON:0001785
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is_a: UBERON:0006843
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intersection_of: UBERON:0006843
2069520686
intersection_of: BFO:0000050 NCBITaxon:10090 ! part of
2069620687
relationship: BFO:0000050 MBA:1009 ! part of fiber tracts
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relationship: BFO:0000050 NCBITaxon:10090 ! part of
@@ -21720,6 +21711,10 @@ property_value: prefLabel "tissue" xsd:string
2172021711
id: UBERON:0000481
2172121712
property_value: prefLabel "multi-tissue structure" xsd:string
2172221713

21714+
[Term]
21715+
id: UBERON:0000482
21716+
property_value: prefLabel "basal lamina of epithelium" xsd:string
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2172321718
[Term]
2172421719
id: UBERON:0000483
2172521720
property_value: prefLabel "epithelium" xsd:string
@@ -23256,6 +23251,10 @@ property_value: prefLabel "mesencephalic tract of trigeminal nerve" xsd:string
2325623251
id: UBERON:0002667
2325723252
property_value: prefLabel "lateral septal nucleus" xsd:string
2325823253

23254+
[Term]
23255+
id: UBERON:0002668
23256+
property_value: prefLabel "oculomotor nerve root" xsd:string
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2325923258
[Term]
2326023259
id: UBERON:0002671
2326123260
property_value: prefLabel "pallidotegmental fasciculus" xsd:string
@@ -24436,6 +24435,10 @@ property_value: prefLabel "trigeminal nerve root" xsd:string
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id: UBERON:0004674
2443724436
property_value: prefLabel "facial nerve root" xsd:string
2443824437

24438+
[Term]
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id: UBERON:0004675
24440+
property_value: prefLabel "hypoglossal nerve root" xsd:string
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2443924442
[Term]
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id: UBERON:0004679
2444124444
property_value: prefLabel "dentate gyrus molecular layer" xsd:string
@@ -25776,10 +25779,6 @@ property_value: prefLabel "future tongue" xsd:string
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id: UBERON:0010059
2577725780
property_value: prefLabel "hypoglossal cord" xsd:string
2577825781

25779-
[Term]
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id: UBERON:0010064
25781-
property_value: prefLabel "open anatomical space" xsd:string
25782-
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[Term]
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id: UBERON:0010083
2578525784
property_value: prefLabel "future dermis" xsd:string
@@ -26008,6 +26007,10 @@ property_value: prefLabel "principal nucleus of stria terminalis" xsd:string
2600826007
id: UBERON:0011179
2600926008
property_value: prefLabel "transverse nucleus of stria terminalis" xsd:string
2601026009

26010+
[Term]
26011+
id: UBERON:0011213
26012+
property_value: prefLabel "root of vagus nerve" xsd:string
26013+
2601126014
[Term]
2601226015
id: UBERON:0011214
2601326016
property_value: prefLabel "nucleus of midbrain tectum" xsd:string
@@ -26432,6 +26435,10 @@ property_value: prefLabel "paraventricular nucleus of the hypothalamus parvocell
2643226435
id: UBERON:0014605
2643326436
property_value: prefLabel "fundus striati" xsd:string
2643426437

26438+
[Term]
26439+
id: UBERON:0014615
26440+
property_value: prefLabel "accessory nerve root" xsd:string
26441+
2643526442
[Term]
2643626443
id: UBERON:0014642
2643726444
property_value: prefLabel "vestibulocerebellum" xsd:string
@@ -26752,6 +26759,14 @@ property_value: prefLabel "sensory organ epithelium" xsd:string
2675226759
id: UBERON:0019306
2675326760
property_value: prefLabel "nose epithelium" xsd:string
2675426761

26762+
[Term]
26763+
id: UBERON:0019310
26764+
property_value: prefLabel "glossopharyngeal nerve root" xsd:string
26765+
26766+
[Term]
26767+
id: UBERON:0019311
26768+
property_value: prefLabel "root of olfactory nerve" xsd:string
26769+
2675526770
[Term]
2675626771
id: UBERON:0020358
2675726772
property_value: prefLabel "accessory XI nerve nucleus" xsd:string

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