major and minor kidney calyces miss-classified as renal venous blood vessel

[dosumis]

This is inferred from the domain of 'drains':

Presumably this relationship was added as a way of indicating urine drainage.

Short term fix:

• remove 'drains' relationships from major and minor calyx terms.

Longer term fixes:

• Check for other potential examples - remove range of drains (for testing purposes only); find terms that are the subject of a drains relationships that are not subclasses of vein.
• Add high level disjoints to catch issues like this in future
• TBD - remove domain of 'drains' in RO?

[RDruzinsky]

Hi, Please forgive me if I have misinterpreted these relationships, but this all seems wrong to me. I don't think that the average anatomist would consider the calyces to be 'part of' the renal pelvis. I suppose if the wall of the calyx is 'part of' the whole space that we call the renal pelvis then I guess it would be correct, but that just seems odd to me. In any case, the problem is not so much that the calyces are 'part of' the renal pelvis. The problem is that the 'drains' relationship is in the Domain vein. The relationship should be 'renal pelvis' drains some 'major calyx' These are not blood vessels. They are vessels for urine. Or am I missing something here? Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 ***@***.*** Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

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On Sun, Mar 6, 2022 at 11:26 AM David Osumi-Sutherland < ***@***.***> wrote: [image: image] <https://user-images.githubusercontent.com/112839/156934304-0a2bc60f-cb47-4b69-bb9a-b856e0ef8fe6.png> This is inferred from the domain of 'drains': [image: image] <https://user-images.githubusercontent.com/112839/156934348-ae1fa66e-dec6-42b1-b070-de21e2dd0b6d.png> It's understandable why this relationships was added. Short term fix: remove 'drains' relationship. Potential longer term fix: remove domain of 'drains' in RO. If the domain of drains is to be kept, we should make more effort to add disjoints that could catch these. — Reply to this email directly, view it on GitHub <#2335>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABASAOEEZZSICM7RLHXFGMLU6TTD5ANCNFSM5QBMHUCA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[dosumis]

Hi Robert,

I don't think that the average anatomist would consider the calyces to be
'part of' the renal pelvis. I suppose if the wall of the calyx is 'part of'
the whole space that we call the renal pelvis then I guess it would be
correct, but that just seems odd to me.

Thanks for the advice. Can you suggest a better alternative partonomy?

The problem is that the 'drains' relationship is in the Domain vein. The relationship should be
'renal pelvis' drains some 'major calyx'
These are not blood vessels. They are vessels for urine.

Agreed. So we need to either broaden the domain of drains, make a new relation or drop recording this functional connectivity relationship.

Cheers,
David

[dosumis]

@bvarner-ebi - please split remaining issues out to new ticket.

[RDruzinsky]

'minor calyx' part of some 'renal sinus' 'major calyx' part of some 'renal sinus' 'renal pelvis' part of some 'renal sinus' 'major calyx' drains some 'minor calyx' 'renal pelvis' drains some 'major calyx' 'ureter' drains some 'renal pelvis' Does this work? Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 ***@***.*** Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

…

On Mon, Mar 7, 2022 at 3:03 AM David Osumi-Sutherland < ***@***.***> wrote: Hi Robert, I don't think that the average anatomist would consider the calyces to be 'part of' the renal pelvis. I suppose if the wall of the calyx is 'part of' the whole space that we call the renal pelvis then I guess it would be correct, but that just seems odd to me. Thanks for the advice. Can you suggest a better alternative partonomy? The problem is that the 'drains' relationship is in the Domain vein. The relationship should be 'renal pelvis' drains some 'major calyx' These are not blood vessels. They are vessels for urine. Agreed. So we need to either broaden the domain of drains, make a new relation or drop recording this functional connectivity relationship. Cheers, David — Reply to this email directly, view it on GitHub <#2335 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABASAOCBTFNL3DZHKGH5653U6XA5DANCNFSM5QBMHUCA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[dosumis]

Renal sinus is classified as a space right now, so not sure this will work. @cmungall - thoughts?

[RDruzinsky]

Instead of 'part of' could we use 'located in' ? Robert E. Druzinsky, Ph.D. Clinical Associate Professor Dept. of Oral Biology College of Dentistry University of Illinois at Chicago 801 S. Paulina Chicago, IL 60612 ***@***.*** Office: 312-996-0406 Lab: 312-996-0629 Website: www.peerj.com/RobertDruzinsky

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On Mon, Mar 7, 2022 at 4:15 PM David Osumi-Sutherland < ***@***.***> wrote: Renal sinus is classified as a space right now, so not sure this will work. @cmungall <https://github.com/cmungall> - thoughts? — Reply to this email directly, view it on GitHub <#2335 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABASAOFW6HASVZWLGEDJS7DU6Z5WTANCNFSM5QBMHUCA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>