NTR insulin concentration measurement assay and data item

[ddooley]

For the new RO paper, a diagram indicating the relationship between diabetic retinopathy, insulin levels and vasoconstriction., needs a few insulin related terms.

We would add this term to the assay template / module:

label: insulin concentration measurement assay definition: A clinical chemistry assay which reports the concentration of insulin in blood. parent: clinical chemistry assay equivalency:

'clinical chemistry assay' 
and realizes some ('analyte role' and 'inheres in' some insulin') 
and realizes some ('evaluant role' and 'inheres in' some blood) 
and 'has specified output' some 'insulin concentration measurement data item'

One issue is that the RO diagram states 'insulin concentration measurement assay' 'has specified input' some blood. Opportunity for 'evaluant role' o 'inheres in' = 'has specified input' ?

This term would go in obi-edit.owl directly:

label: insulin concentration measurement data item definition: A measurement datum which is the concentration of insulin in blood. parent: measurement datum axiom: 'specified output of' some 'insulin concentration measurement assay'

[bpeters42]

Thanks Damion, the diagram is awesome!

For the assay, we should add it to the assay template. If it isn't in there already, the template should specify that all 'evaluants' are both specified inputs, and bearers of the evaluant role (which is realized in the assay).

For the data item, we are obviously running into the fact that we still don't have a perfect way of modeling them. But I would be hesitant to just create the class, given that - no matter what solution we will ultimately have - we do not want to pre-compose all possible types of measurement data in OBI. So can we instead label the output as 'measurement datum', and point from that item to 'insulin concentration' ?

I hope this makes sense.

• Bjoern

On Thu, Mar 25, 2021 at 7:31 PM Damion Dooley @.***> wrote:

For the new RO paper, a diagram indicating the relationship between diabetic retinopathy, insulin levels and vasoconstriction., needs a few insulin related terms.

[image: image] https://user-images.githubusercontent.com/4000582/112585137-77e51c00-8db6-11eb-8d68-12025a79fd29.png

We would add this term to the assay template / module:

label: insulin concentration measurement assay definition: A clinical chemistry assay which reports the concentration of insulin in blood. parent: clinical chemistry assay equivalency:

'clinical chemistry assay' and realizes some ('analyte role' and 'inheres in' some insulin') and realizes some ('evaluant role' and 'inheres in' some blood) and 'has specified output' some 'insulin concentration measurement data item'

One issue is that the RO diagram states 'insulin concentration measurement assay' 'has specified input' some blood. Opportunity for 'evaluant role' o 'inheres in' = 'has specified input' ?

This term would go in obi-edit.owl directly:

label: insulin concentration measurement data item definition: A measurement datum which is the concentration of insulin in blood. parent: measurement datum axiom: 'specified output of' some 'insulin concentration measurement assay'

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[ddooley]

Sure, I like that general solution for having the assay output a 'measurement datum'. Now did you mean to introduce a new term 'insulin concentration'? It looks like all the PATO 'concentration of x' terms have pattern 'concentration of x in y' so we'd be looking at 'concentration of insulin in blood'. Looks like OBI doesn't have 'concentration of x in y' terms at moment.

[cstoeckert]

Note that http://purl.obolibrary.org/obo/OBI_0003223 'insulin concentration assay' already exists in OBI.

[ddooley]

Great, somehow I'd missed that, it didn't come up in RO paper discussion. Also I just learned from Kai that the "concentration of x in y" was actually borrowed from ENVO where it was a pattern developed in consult with Chris Mungall. However there "inheres in" is used, but COB now uses "characteristic of". Here's an example using selenium:

I'll try it out in a version of diagram to see if it garners support in this context.

d.

[ddooley]

So we've simplified the diagram, and not precomposed a "insulation concentration measurement data item". Closing this.