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hubmapconsortium · Nov 7, 2022 · 1f2409e · 1f2409e
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diff --git a/NOTES.md b/NOTES.md
@@ -7,6 +7,7 @@ Release Notes
 |Ontology|Version|
 | :---: | :---: |
 |CL|2022-09-15|
+|PCL|2022-10-19|
 |UBERON|2022-09-30|
 
 ### ASCT+b Tables
@@ -64,4 +65,4 @@ Release Notes
 |Ureter|NA|revise for April 2023|
 |Urinary_bladder|v1.1|revise for April 2023|
 |Uterus|v1.2|revise for October 1, 2022|
-|Blood_vasculature|v1.3|2022-09-28|
+|Blood_vasculature|v1.3|2022-10-25|
diff --git a/graphs/ccf_Blood_graph.pdf b/graphs/ccf_Blood_graph.pdf
diff --git a/graphs/ccf_Blood_vasculature_graph.pdf b/graphs/ccf_Blood_vasculature_graph.pdf
diff --git a/graphs/ccf_Bone-Marrow_graph.pdf b/graphs/ccf_Bone-Marrow_graph.pdf
diff --git a/graphs/ccf_Brain_graph.pdf b/graphs/ccf_Brain_graph.pdf
diff --git a/graphs/ccf_Brain_graph.png b/graphs/ccf_Brain_graph.png
diff --git a/graphs/ccf_Eye_graph.pdf b/graphs/ccf_Eye_graph.pdf
diff --git a/graphs/ccf_Eye_graph.png b/graphs/ccf_Eye_graph.png
diff --git a/graphs/ccf_Fallopian_tube_graph.pdf b/graphs/ccf_Fallopian_tube_graph.pdf
diff --git a/graphs/ccf_Heart_graph.pdf b/graphs/ccf_Heart_graph.pdf
diff --git a/graphs/ccf_Kidney_graph.pdf b/graphs/ccf_Kidney_graph.pdf
diff --git a/graphs/ccf_Kidney_graph.png b/graphs/ccf_Kidney_graph.png
diff --git a/graphs/ccf_Knee_graph.pdf b/graphs/ccf_Knee_graph.pdf
diff --git a/graphs/ccf_Large_intestine_graph.pdf b/graphs/ccf_Large_intestine_graph.pdf
diff --git a/graphs/ccf_Large_intestine_graph.png b/graphs/ccf_Large_intestine_graph.png
diff --git a/graphs/ccf_Liver_graph.pdf b/graphs/ccf_Liver_graph.pdf
diff --git a/graphs/ccf_Lung_graph.pdf b/graphs/ccf_Lung_graph.pdf
diff --git a/graphs/ccf_Lung_graph.png b/graphs/ccf_Lung_graph.png
diff --git a/graphs/ccf_Lymph_node_graph.pdf b/graphs/ccf_Lymph_node_graph.pdf
diff --git a/graphs/ccf_Lymph_vasculature_graph.pdf b/graphs/ccf_Lymph_vasculature_graph.pdf
diff --git a/graphs/ccf_Ovary_graph.pdf b/graphs/ccf_Ovary_graph.pdf
diff --git a/graphs/ccf_Pancreas_graph.pdf b/graphs/ccf_Pancreas_graph.pdf
diff --git a/graphs/ccf_Peripheral_nervous_system_graph.pdf b/graphs/ccf_Peripheral_nervous_system_graph.pdf
diff --git a/graphs/ccf_Placenta_graph.pdf b/graphs/ccf_Placenta_graph.pdf
diff --git a/graphs/ccf_Prostate_graph.pdf b/graphs/ccf_Prostate_graph.pdf
diff --git a/graphs/ccf_Skin_graph.pdf b/graphs/ccf_Skin_graph.pdf
diff --git a/graphs/ccf_Small_intestine_graph.pdf b/graphs/ccf_Small_intestine_graph.pdf
diff --git a/graphs/ccf_Spleen_graph.pdf b/graphs/ccf_Spleen_graph.pdf
diff --git a/graphs/ccf_Thymus_graph.pdf b/graphs/ccf_Thymus_graph.pdf
diff --git a/graphs/ccf_Thymus_graph.png b/graphs/ccf_Thymus_graph.png
diff --git a/graphs/ccf_Ureter_graph.pdf b/graphs/ccf_Ureter_graph.pdf
diff --git a/graphs/ccf_Urinary_bladder_graph.pdf b/graphs/ccf_Urinary_bladder_graph.pdf
diff --git a/graphs/ccf_Uterus_graph.pdf b/graphs/ccf_Uterus_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Blood_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Blood_vasculature_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Blood_vasculature_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Bone-Marrow_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Brain_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Brain_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Brain_graph.png b/graphs/last_official_ASCTB_release/ccf_Brain_graph.png
diff --git a/graphs/last_official_ASCTB_release/ccf_Eye_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Eye_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Eye_graph.png b/graphs/last_official_ASCTB_release/ccf_Eye_graph.png
diff --git a/graphs/last_official_ASCTB_release/ccf_Fallopian_tube_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Fallopian_tube_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Heart_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Heart_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Kidney_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Kidney_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Kidney_graph.png b/graphs/last_official_ASCTB_release/ccf_Kidney_graph.png
diff --git a/graphs/last_official_ASCTB_release/ccf_Knee_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Knee_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Large_intestine_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Large_intestine_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Liver_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Liver_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lung_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lung_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lung_graph.png b/graphs/last_official_ASCTB_release/ccf_Lung_graph.png
diff --git a/graphs/last_official_ASCTB_release/ccf_Lymph_node_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lymph_node_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Lymph_vasculature_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Lymph_vasculature_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Ovary_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Ovary_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Pancreas_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Pancreas_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Peripheral_nervous_system_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Peripheral_nervous_system_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Placenta_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Placenta_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Prostate_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Prostate_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Skin_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Skin_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Small_intestine_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Small_intestine_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Spleen_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Spleen_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Thymus_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Thymus_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Ureter_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Ureter_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Urinary_bladder_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Urinary_bladder_graph.pdf
diff --git a/graphs/last_official_ASCTB_release/ccf_Uterus_graph.pdf b/graphs/last_official_ASCTB_release/ccf_Uterus_graph.pdf
diff --git a/logs/Large_intestine_AS_CT_strict_log.tsv b/logs/Large_intestine_AS_CT_strict_log.tsv
diff --git a/logs/class_Brain_indirect_log.tsv b/logs/class_Brain_indirect_log.tsv
@@ -11,15 +11,19 @@ UBERON:0001908	optic tract	optic tract	UBERON:0019261	white matter of forebrain
 UBERON:0002023	claustrum of brain	claustrum	UBERON:0019264	gray matter of forebrain	gray matter of forebrain
 UBERON:0002028	hindbrain	hindbrain (rhombencephalon)	UBERON:0000955	brain	brain
 UBERON:0002151	pontine nuclear group	basilar part of pons (Pontine nuclei)	UBERON:0000988	pons	pons
+UBERON:0002152	middle cerebellar peduncle	middle cerebellar peduncle	UBERON:0019258	white matter of hindbrain	white matter of hindbrain
+UBERON:0002163	inferior cerebellar peduncle	inferior cerebellar peduncle	UBERON:0019258	white matter of hindbrain	white matter of hindbrain
 UBERON:0002265	olfactory tract	olfactory tract	UBERON:0019261	white matter of forebrain	white matter of forebrain
 UBERON:0002476	lateral globus pallidus	globus pallidus, external	UBERON:0010011	collection of basal ganglia	basal nuclei (basal ganglia)
 UBERON:0002477	medial globus pallidus	globus pallidus, internal	UBERON:0010011	collection of basal ganglia	basal nuclei (basal ganglia)
 UBERON:0002564	lateral orbital gyrus	lateral orbital gyrus	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0002570	medial orbital gyrus	medial orbital gyrus	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0002593	orbital operculum	orbital operculum	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0002603	paraterminal gyrus	paraterminal gyrus	UBERON:0002600	limbic lobe	limbic lobe
-UBERON:0002644	intermediate orbital gyrus	posterior intermediate orbital gyrus	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0002644	intermediate orbital gyrus	anterior intermediate orbital gyrus	UBERON:0016525	frontal lobe	frontal lobe
+UBERON:0002644	intermediate orbital gyrus	posterior intermediate orbital gyrus	UBERON:0016525	frontal lobe	frontal lobe
+UBERON:0002651	anterior horn of lateral ventricle	anterior horn of lateral ventricle	UBERON:0002285	telencephalic ventricle	lateral ventricles
+UBERON:0002655	body of lateral ventricle	body of lateral ventricle	UBERON:0002285	telencephalic ventricle	lateral ventricles
 UBERON:0002661	superior frontal gyrus	superior frontal gyrus	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0002702	middle frontal gyrus	middle frontal gyrus	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0002703	precentral gyrus	precentral gyrus	UBERON:0016525	frontal lobe	frontal lobe
@@ -28,6 +32,7 @@ UBERON:0002947	frontal operculum	frontal operculum	UBERON:0016525	frontal lobe	f
 UBERON:0002948	superior occipital gyrus	superior occipital gyrus	UBERON:0002021	occipital lobe	occipital lobe
 UBERON:0002998	inferior frontal gyrus	inferior frontal gyrus	UBERON:0016525	frontal lobe	frontal lobe
 UBERON:0003017	substantia innominata	substantia Innominata	UBERON:0002743	basal forebrain	basal forebrain
+UBERON:0004672	posterior horn lateral ventricle	posterior horn of lateral ventricle	UBERON:0002285	telencephalic ventricle	lateral ventricles
 UBERON:0004720	cerebellar vermis	cerebellar vermis	UBERON:0002037	cerebellum	cerebellum
 UBERON:0006092	cuneus cortex	cuneus	UBERON:0002021	occipital lobe	occipital lobe
 UBERON:0007769	medial preoptic region	preoptic region	UBERON:0001898	hypothalamus	hypothalamus

diff --git a/logs/class_Brain_log.tsv b/logs/class_Brain_log.tsv
@@ -14,8 +14,6 @@ UBERON:0001947	red nucleus	red nucleus	UBERON:0019267	gray matter of midbrain	gr
 UBERON:0002037	cerebellum	cerebellum	UBERON:0019263	gray matter of hindbrain	gray matter of hindbrain
 UBERON:0002038	substantia nigra	substantia nigra	UBERON:0019267	gray matter of midbrain	gray matter of midbrain
 UBERON:0002150	superior cerebellar peduncle	superior cerebellar peduncle	UBERON:0019258	white matter of hindbrain	white matter of hindbrain
-UBERON:0002152	middle cerebellar peduncle	middle cerebellar peduncle	UBERON:0019258	white matter of hindbrain	white matter of hindbrain
-UBERON:0002163	inferior cerebellar peduncle	inferior cerebellar peduncle	UBERON:0019258	white matter of hindbrain	white matter of hindbrain
 UBERON:0002264	olfactory bulb	Olfactory bulb	UBERON:0002600	limbic lobe	limbic lobe
 UBERON:0002291	central canal of spinal cord	central canal of medulla oblongata	UBERON:0004086	brain ventricle	ventricles of hindbrain
 UBERON:0002590	prepyriform area	prepiriform region	UBERON:0002600	limbic lobe	limbic lobe

diff --git a/logs/class_Eye_indirect_log.tsv b/logs/class_Eye_indirect_log.tsv
@@ -13,6 +13,7 @@ UBERON:0000966	retina	retina	UBERON:0000970	eye	eye
 UBERON:0001769	iris	iris	UBERON:0000970	eye	eye
 UBERON:0001772	corneal epithelium	corneal epithelium	UBERON:0000964	Cornea	Cornea
 UBERON:0001775	ciliary body	ciliary body	UBERON:0000970	eye	eye
+UBERON:0001776	optic choroid	optic choroid	UBERON:0002203	vasculature of eye	vasculature of eye
 UBERON:0001782	pigmented layer of retina	retinal pigmented epithelium	UBERON:0000966	retina	retina
 UBERON:0001789	outer nuclear layer of retina	outer nuclear layer	UBERON:0000966	retina	retina
 UBERON:0001791	inner nuclear layer of retina	inner nuclear layer	UBERON:0000966	retina	retina

diff --git a/logs/class_Eye_log.tsv b/logs/class_Eye_log.tsv
@@ -21,6 +21,5 @@ CL:0011005	GABAergic interneuron	GABAergic interneuron	CL:0000561	Amacrine Cell
 CL:0011107	obsolete Muller cell	Muller glia	CL:0000540	neuron	Neuron
 CL:0011107	obsolete Muller cell	Muller glia	UBERON:0001791	inner nuclear layer of retina	inner nuclear layer
 CL:0017004	telocyte	telocyte	UBERON:0003952	anterior stroma of cornea	anterior stroma of cornea
-UBERON:0001776	optic choroid	optic choroid	UBERON:0002203	vasculature of eye	vasculature of eye
 UBERON:0002203	vasculature of eye	vasculature of eye	UBERON:0000966	retina	retina
 UBERON:0006762	suspensory ligament of lens	ciliary zonules	UBERON:0000965	lens of camera-type eye	lens
diff --git a/logs/class_Kidney_indirect_log.tsv b/logs/class_Kidney_indirect_log.tsv
@@ -1,14 +1,14 @@
 s	slabel	user_slabel	o	olabel	user_olabel
-UBERON:0001225	cortex of kidney	cortex of kidney	UBERON:0002113	kidney	kidney
 UBERON:0001225	cortex of kidney	renal cortex	UBERON:0002113	kidney	kidney
+UBERON:0001225	cortex of kidney	cortex of kidney	UBERON:0002113	kidney	kidney
 UBERON:0001228	renal papilla	Papilla	UBERON:0002113	kidney	kidney
 UBERON:0001231	nephron tubule	Tubules	UBERON:0001285	nephron	nephron
 UBERON:0001285	nephron	nephron	UBERON:0002113	kidney	kidney
 UBERON:0001289	descending limb of loop of Henle	Loop of Henle (Thin Limb)	UBERON:0001231	nephron tubule	Tubules
-UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/ Cortex)	UBERON:0001231	nephron tubule	Tubules
-UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/Medulla)	UBERON:0001231	nephron tubule	Tubules
-UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/Cortex)	UBERON:0001231	nephron tubule	Tubules
 UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb)	UBERON:0001231	nephron tubule	Tubules
+UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/Cortex)	UBERON:0001231	nephron tubule	Tubules
+UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/Medulla)	UBERON:0001231	nephron tubule	Tubules
+UBERON:0001291	thick ascending limb of loop of Henle	Loop of Henle (Thick Limb/ Cortex)	UBERON:0001231	nephron tubule	Tubules
 UBERON:0001292	distal convoluted tubule	Distal Convolution	UBERON:0001231	nephron tubule	Tubules
 UBERON:0002015	kidney capsule	kidney capsule	UBERON:0002113	kidney	kidney
 UBERON:0003527	kidney capillary	Kidney Capillary	UBERON:0001981	blood vessel	Blood Vessel