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Add albumin-free serum #1762

Merged
merged 2 commits into from
Mar 18, 2024
Merged

Add albumin-free serum #1762

merged 2 commits into from
Mar 18, 2024

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sebastianduesing
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@sebastianduesing sebastianduesing commented Jan 26, 2024

Closes #493. Adds "albumin-free serum."

The diff on this is weirdly big, and I'm not sure why. The ROBOT diff is clean. We can discuss in next OBI call—if there's a reason why this one turned out so messy, I'll re-do this PR.

Editing to add: James said the messy diff is probably OWL API issue, but it looked benign. To discuss on call: the logical axiom "blood serum specimen and (has part only (not albumin))".

@cmungall
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cmungall commented Mar 2, 2024

I dunno how you ended up with genids, maybe from CLO. If you don't get rid of them they wll continue to cause churn

(of course robot diff by design shows no change as there is no change at the OWL axiom level)

@cmungall
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cmungall commented Mar 4, 2024

It looks like OBI is interested in modeling media mixtures as might be found in e.g sigma aldritch catalog

Is there a document with the design patterns documented? I think you will encounter issues with OWL quantification further down the line. I have a general interest in this area and in ontological representation of media mixes for microbial culturing, and am planning to use chemrof:ChemicalMixture as DPs for hierarchical quantification of both precise and imprecise mixtures. You can ignore my comment for the purposes of this PR though, just an expression of interest. cc @realmarcin

Some relevant papers:

@turbomam
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turbomam commented Mar 4, 2024

I did some experimentation with this new class in

I never accomplished what I had hoped for, but that doesn't mean I have any objection to this PR

@sebastianduesing
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@cmungall I just put together a pull request (#1769) to remove the genids. They were related to OBI:0100061, which had an editor note attached to one axiom; switching that to a general editor note annotation got rid of the genids.

Thanks for the interest in the issue of modeling mixtures. That's a topic that @ddooley and I will likely be working on in our material processing ontology project, though that's still in the early stages. Agreed that OWL quantification will be challenging.

@jamesaoverton jamesaoverton merged commit c316819 into master Mar 18, 2024
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@jamesaoverton jamesaoverton deleted the albumin-free-serum-493 branch March 18, 2024 19:37
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albumin free serum
4 participants