Harmonise logical definitions of "Calcified Anatomy" terms

[matentzn]

@pnrobinson @nicolevasilevsky @LCCarmody I invited you to work on the calcification phenotypes here: https://docs.google.com/spreadsheets/d/1IMSucZiqWYfPvp-m2x74IcE84xXV57mzz9rSNYZQLbc/edit#gid=0

Basically what I need to proceed:

1. an anatomical entity in every row C
2. I dont care about D, but i suggest you also do that to make reviewing this easier
3. For punctate and similar calcification, fill in E (not for simple calcifications!)
4. Not necessary, but for transparency, I would like the pattern name in the G column. If too much work, no need!

What is in that table?

1. Every phenotype that has "calcif" in the label
2. Every phenotype that currently matches "calcifiedAnatomicalEntity" pattern

So there will be some calcification phenotypes missing (those that don't have calcif in the name. If you see them when playing around, just add them to the table. Good luck and let me know when its done!

Originally posted by @matentzn in https://github.com/obophenotype/human-phenotype-ontology/issues/4844#issuecomment-773238940

Action items (in that order)

• [x] @LCCarmody to finish table as far as she can
• [X] @LCCarmody @matentzn Update/add definitions of calcifiedAnatomicalEntity in HPO
• [X] Add pattern calcifiedAnatomicalEntityByCalcificationPattern
• [x] @LCCarmody submit pattern to uPheno
• [x] @LCCarmody add this to our meeting minutes TODO

[pnrobinson]

any progress here? @LCCarmody @matentzn -- I'd love to clean up all of the old issues!

[matentzn]

Removing EQs without replacement: Missing pattern and/of Uberon terms:

• HP:0004966 (Medial calcification of large arteries): No way to express "large arteries"

I think there are still some uncertainties in that spreadsheet. @LCCarmody can you separate the questions by domain:

• Questions of the kind "is this the right Uberon term" (uPheno repo issue)
• Questions of the kind "is this the right PATO term" (uPheno repo issue)
• Other questions: Email to hpo editors list.

Action item:

• [ ] @LCCarmody to tell Nico when the spreadsheet has no more uncertainties or comments in it :)

Thanks!

[LCCarmody]

Don't think we will make EQs for the following terms because it may take too much time to determine subcategories.

-- | -- HP:0012457 | Medial calcification of medium-sized arteries HP:0012458 | Medial calcification of small arteries HP:0031301 | Peripheral arterial calcification HP:0031302 | Lower extremity peripheral arterial calcification HP:0004966 | Medial calcification of large arteries

HP:0007238	Nonarteriosclerotic cerebral calcification

[matentzn]

@pnrobinson please check whether the following anatomy assignments are reasonable for the EQs:

• [ ] HP:0007045 | Midline brain calcifications | UBERON:1000009 | midline crest NO !!!!!! This would be brain and then PATO middle or something like that.
• [x] HP:0007346 | Subcortical white matter calcifications | UBERON:0011299 | white matter of telencephalon NO !!!! This would probably need a new PATO term for subcortical ("underneath" the cerebral cortex"), it is not a well defined anatomical thing that we would have in UBERON
• [x] HP:0031306 | Intracranial arterial calcification | UBERON:0011362 | cranial blood vasculature?? NO !! THis is just the arteries. Consider a new UBERON term for cranial arteries?
• [x] HP:0025477 | Periarticular calcification | UBERON:0000982 | skeletal joint YES
• [x] HP:0033538 | Aortic annulus calcification | UBERON:0005991 | aortic valve anulus (is anulus spelled correctly? where?) YES (Annulus with two "n" is the correct spelling, even though etymologically it should have been anulus)
• [x] HP:0007229 | Intracerebral periventricular calcifications | UBERON:0014932 | periventricular white matter YES

[LCCarmody]

After discussion with @matentzn, decided not to patternize

Modifier
HP:0006906	Congenital intracerebral calcification	UBERON:0001893	telencephalon	HP_0003577	congenital onset	calcifiedAnatomicalEntitybyOnset	Not sure this is worth a pattern
HP:0006694	Early progressive calcific cardiac valvular disease	UBERON:0000946	cardial valve	HP_0003676	progressive	calcifiedAnatomicalEntitybyOnset	There isn't an 'early progressive' term
HP:0005849	Diffuse cerebral calcification	UBERON:0001893	telencephalon	PATO:0001566	distributed	calcifiedAnatomicalEntityByCalcificationType	distributed has 'diffuse' as synonym
HP:0011084	Hypocalcification of dental enamel	UBERON:0005176	tooth enamel organ	PATO:0001672	decreased distribution	calcifiedAnatomicalEntityByCalcificationType	Not sure if this is the correct modifyer
HP:0005671	Bilateral intracerebral calcifications	UBERON:0001893	telenceophalon	HP_0012832	bilateral	calcifiedAnatomicalEntityByPosition	Not sure if this is worth a pattern

[pnrobinson]

@matentzn @LCCarmody what is the action item here?

[matentzn]

@pnrobinson because I also keep asking that question, I have recently started to encourage the use of checkbox syntax:

• [ ] Example checkbox

To show action items. You can scroll through this ticket and see all of these, on who they are assigned to (some to you!)

[pnrobinson]

OK, but note the checkbox syntax is not great if there is a series of questions that require an answer -- see above!

[matentzn]

Ah ok, so now its for @LCCarmody do sort this out - I see you edited my comment with your questions. I did not see that before!

[LCCarmody]

Hi @matentzn I am not sure what you mean by I edited your comment with my questions. BUT I think this ticket should be closed because we cannot patternize the remaining terms. Either they are very complicated or there isn't a good term in UBERON (see https://github.com/obophenotype/uberon/issues/1933).

[matentzn]

I meant that Peter has edited my todolist with comments - these should perhaps be addressed as it looks like we may have added some wrong fillers somewhere? Maybe I am just daft and then, feel free to close.

[dosumis]

Just looking at this with @rays22 as he's encountered some of these patterns while looking for newuPheno patterns. We'd like to track down: calcifiedAnatomicalEntityByCalcificationPattern. The checkbox says it's done but a search of the uPheno repo doesn't pull it up. (This is the reason I don't like checkboxes).

[matentzn]

I think thats it: https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/patterns/dosdp-patterns/calcifiedAnatomicalEntityWithCalcificationPattern.yaml

[dosumis]

Ta. Assumed it would be on uPheno.

[matentzn]

Yeah, that checkbox wasnt checked yet :) @LCCarmody will probably do that at some point?

[LCCarmody]

Sorry, still having trouble following this thread. I did read the old comments, but I think my brain is slow. What exactly will I do at some point? Suggestions:

1. implement https://github.com/obophenotype/human-phenotype-ontology/blob/master/src/patterns/dosdp-patterns/calcifiedAnatomicalEntityWithCalcificationPattern.yaml into HPO?
2. implement https://github.com/obophenotype/upheno/issues/813 in upheno? FTR, I've edited upheno patterns, but I am not exactly sure what the action beyond that is. I will comment on that ticket.
3. or check a box?

It seems @rays22 beat me to 2, so maybe he should check the box?

Also, ftr, I finally got a computer that can actually do things...like run releases, etc. So, I will work on updating/editing ontologies soon, but I'm mighty rusty. :)

[matentzn]

@LCCarmody From my perspective I would:

• Make sure that you fix all the EQs mentioned in the comment above where Peter commented (most of our suggestions were wrong)
• Then make sure all calcified punctate classes adhere to the uPheno pattern we prepared.

Ping me on slack if you have trouble with any of these! We are also way overdue a meeting!

[LCCarmody]

Okay, sorry, finally getting around to adding starting the PR. One question about HP:0007045 | Midline brain calcifications (see above comment). Would this be an appropriate def? or should we leave without a def? @rays22 @matentzn

'has part' some (calcified ('medial orientation' and ('characteristic of' some brain) and ('has modifier' some abnormal) and ('has modifier' some punctate))

 where medial orientation is http://purl.obolibrary.org/obo/PATO_0002498

[matentzn]

@rays22 can you give it a shot to model as an EQ?

[rays22]

Need new UBERON term 'brain midline'?

[pnrobinson]

@LCCarmody @rays22 the above definition (April 21) seemed OK -- I do not think that there is actually a defineable and delineable region for brain midline -- it does not seem that it would be a great uberon term

[LCCarmody]

Actually, I used the term 'midline crest' in pull request #7599, which is defined as "A ridge or peak located along the middle part of the head, located approximately equidistant from the left and the right sides of the head. "

If this is not correct, then it should be edited in the HP--as the pull request was approved. I should have closed this ticket, but I seem to have forgotten.