Replace supplies and drains relations by more specific relations
#3426
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RO now provides 'vessel supplies blood to' (RO:0020101) as a more specific variant of 'supplies' (RO:0002178). The new relation is domain-restricted to 'blood vessel' (UBERON:0001981). We use that new relation wherever 'supplies' was used to qualify a blood vessel. Likewise for 'vessel drains blood from' (RO:0020102), which is a more specific variant of 'drains' (RO:0002179). Recently introduced patterns for arteries and veins (#3288) already use the more specific relations. No longer using 'drains' and 'supplies' wherever a blood vessel is involved means that we no longer need to inject our own domain and range restrictions to those relations, so we remove those injections as well (#2453).
'supraorbital artery' (UBERON:0015160) supplies blood to the 'frontal sinus' (UBERON:0001760), but 'frontal sinus' represents an immaterial anatomical cavity, and is therefore incompatible with the range restriction of the 'vessel supplies blood to' (RO:0020101) relation. We replace the object of that relation to 'mucosa of frontal sinus' (a material anatomical entity) instead.
The 'intercostal vein' (UBERON:0012197) and 'intercostal artery' (UBERON:0005612) are said to drain and supply blood from and to the 'intercostal space' (UBERON:0012198). In both cases, this violates the range restriction of the 'vessel drains blood from' (RO:0020102) and 'vessel supplies blood to' (RO:0020101) relations, because 'intercostal space' is an immaterial anatomical entity. We create a new term 'intercostal element' intended to refer to any anatomical structure located within an intercostal space (e.g. intercostal muscles, intercostal lymph nodes), and use the new term to replace 'intercostal space' in the relationships with 'intercostal vein' and 'intercostal arteries'.
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
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Suggestion from Uberon December 16th meeting: No need for an “intercostal element“, just re-define |
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Superseded by #3450. |
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RO now provides 'vessel supplies blood to' (RO:0020101) as a more specific variant of 'supplies' (RO:0002178). The new relation is domain-restricted to 'blood vessel' (UBERON:0001981). In this PR, we use the new relation wherever 'supplies' was used to qualify a blood vessel.
Likewise for 'vessel drains blood from' (RO:0020102), which is a more specific variant of 'drains' (RO:0002179).
Recently introduced patterns for arteries and veins (in #3288) already use the more specific relations, so this improves Uberon’s consistency. More importantly, no longer using 'supplies' and 'drains' wherever a blood vessel is involved means that we no longer need to inject our own domain restrictions to those relations, so we can remove those injections as well (#2453).
The new relations are range-restricted in RO to (material) 'anatomical structure', which causes two side-effects:
'supraorbital artery' (UBERON:0015160) is unsatisfiable because it 'supplies blood to' the 'frontal sinus' (UBERON:0001760), which is an immaterial entity. We fix that by changing the target of the relation to 'mucosa of frontal sinus' (UBERON:0005027).
'intercostal vein' (UBERON:0012197) and 'intercostal artery' (UBERON:0005612) are unsatisfiable because they drain and supply blood from and to the 'intercostal space' (UBERON:0012198), an immaterial entity. As proposed in this comment, we fix that by introducing a new term 'intercostal element', intended to cover any anatomical entity located within an intercostal space.