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Object property

Uses

​

part of

8105

​

branching part of

183

​

bounding layer of

25

​

luminal space of

2

​

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Object property

Uses

overlaps

286

conduit for

33

contributes to morphology of

650

has part

673

composed primarily of

193

part of

8142

bounding layer of

25

branching part of

74

lumen of

0

luminal space of

2

Only Uberon is represented, we need CL

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Safe properties for grouping

Partly safe for grouping

Unsafe properties for grouping

part of

overlaps

connected to

bounding layer of

contributes to morphology of

connecting branch of

branching part of

​

drains

lumen of

​

supplies

luminal space of

​

continuous with

​

​

surrounds

​

​

has part

​

​

composed primarily of

​

​

conduit for

​

​

attached to

Only Uberon is represented, we need CL

4 of 18

nephron tubule

loop of Henle

ascending limb thin segment

descending limb

of loop of Henle

nephron tubule

loop of Henle

ascending limb

thin segment

​

renal connecting

tubule

descending limb

of loop of Henle

region of

nephron tubule

loop of Henle

SUBCLASSOF

SUBCLASSOF

SUBCLASSOF

part of

SUBCLASSOF

SUBCLASSOF

renal connecting

tubule

SUBCLASSOF

part of

SUBCLASSOF

SUBCLASSOF

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6 of 18

7 of 18

8 of 18

nephron tubule

loop of Henle

ascending limb thin segment

descending limb

of loop of Henle

region of

nephron tubule

loop of Henle

SUBCLASSOF

SUBCLASSOF

part of

SUBCLASSOF

SUBCLASSOF

renal connecting

tubule

SUBCLASSOF

part of

nephron tubule

loop of Henle

ascending limb

thin segment

​

renal connecting

tubule

descending limb

of loop of Henle

SUBCLASSOF

SUBCLASSOF

SUBCLASSOF

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TBA - Panel showing renal corpuscle graph with terms in view highlighted

10 of 18

renal corpuscle

glomerular parietal epithelium / epithelial cell

glomerular visceral epithelium / epithelial cell (podocyte)

glomerular (capillary) endothelium

mesangium / mesangial cell

​

​

afferent arteriole

efferent arteriole

Credit: KPMP

A

B

D

C

D

11 of 18

ovary

ovary septum

oviduct

ovarian ligament

ovarian vein

ovarian artery

part of

connects

drains

supplies

attached to

AS 1 LABEL

AS 1 ID

AS 2 LABEL

AS 2 ID

AS 3 LABEL

AS 3 ID

AS 4 LABEL

AS 4 ID

CT 1 LABEL

CT 1 ID

kidney

UBERON:0002113

kidney vasculature

UBERON:0006544

kidney blood vessel

UBERON:0003517

endothelium

UBERON:0001986

peritubular capillary endothelial cell

CL:1001033

kidney

UBERON:0002113

kidney vasculature

UBERON:0006544

kidney blood vessel

UBERON:0003517

endothelium

UBERON:0001986

vasa recta descending limb cell

CL:1001285

kidney

UBERON:0002113

kidney vasculature

UBERON:0006544

kidney blood vessel

UBERON:0003517

endothelium

UBERON:0001986

vasa recta ascending limb cell

CL:1001131

AS 1 LABEL

AS 1 ID

…

AS 4 LABEL

AS 4 ID

CT 1 LABEL

CT 1 ID

kidney

UBERON:0002113

…

endothelium

UBERON:0001986

peritubular capillary endothelial cell

CL:1001033

kidney

UBERON:0002113

…

endothelium

UBERON:0001986

vasa recta descending limb cell

CL:1001285

kidney

UBERON:0002113

…

endothelium

UBERON:0001986

vasa recta ascending limb cell

CL:1001131

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Brainstorming making figure for HDCA:

  • Given that this is preliminary work, we can cherry pick a few examples of cases where mapping is useful for distinguishing grouping relationships from non-grouping ones
  • We can emphasis that hierarchies that don't have any simple match to our semantics can still be preserved by the pipeline as annotation hierarchies
  • Find some examples of developmental relationships that validate (neural crest to Pharyngeal arch works
  • Make view generation examples - which shows addition of missing relationships (might be slow to find examples)

13 of 18

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https://link.springer.com/chapter/10.1007/978-3-031-15636-6_2

15 of 18

https://embryology.ch/en/organogenesis/digestion-tract/face-and-upper-foregut/introduction.html

16 of 18

A

B

17 of 18

Request figures

  • I have obtained the EBI Tax ID that is required
  • I have created an account for ccc right link
  • Probably better to finish requesting whenever we an expected publication date

18 of 18

AS1

AS2

AS3

AS4

Neural crest

Pharyngeal arch

Pharyngeal arch 1

Mandible

Neural crest

Pharyngeal arch

Pharyngeal arch 1

Maxilla

A

D

C

B

P1

P2

P3