Review: increasedImmunoglobulinComplexAgainstEntity

[srobb1]

increasedImmunoglobulinComplexAgainstEntity.yaml

Is it okay for the patterns to not have an equivalentTo?

[matentzn]

@nicolevasilevsky, this pattern is not a uPheno pattern right? Is this used at all? If so, can I move it to HP or some more suitable location?

[nicolevasilevsky]

it is just used in HPO, not sure if other phenotype ontologies would want to adapt it (like MP?)

Feel free to move it the HPO repo.

[matentzn]

@cmungall can you check this pattern and see whether there is a RO relation that could reflect the relationship of the antibody against the target? @nicolevasilevsky could you clarify what kind of targets we are talking about here?

[cmungall]

Let's start by restricting the filler from BFO entity - what kinds of things to the antibodies target?

On Thu, Feb 14, 2019 at 4:22 AM Nico Matentzoglu notifications@github.com wrote:

@cmungall https://github.com/cmungall can you check this pattern and see whether there is a RO relation that could reflect the relationship of the antibody against the target? @nicolevasilevsky https://github.com/nicolevasilevsky could you clarify what kind of targets we are talking about here?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/obophenotype/upheno/issues/347#issuecomment-463607824, or mute the thread https://github.com/notifications/unsubscribe-auth/AADGObCwqUsfb_vEaPfrW-_1blWgQPPZks5vNVUDgaJpZM4axP4L .

[mellybelly]

pls look at the antibody ontology work that @mbrush did, we defined all these targets.

[nicolevasilevsky]

@mellybelly @mbrush where can we find all the antibody ontology work? is it in a repo somewhere?

@matentzn and @cmungall you can see the antibody targets that are in HPO here: https://hpo.jax.org/app/browse/term/HP:0003212

There are terms for anti-protein, organism, anatomical entities (anti-feather), plants, etc. antibodies

[matentzn]

So if this can be anything, it does sound like the domain should be material entity? Is that correct?

[matentzn]

Nicole comment elsewhere: "the targets can really be anything that is seen as 'foreign' and your body would develop antibodies against, like drugs, proteins, organisms (like dust mites), etc. I know this is pattern isn't a typical pattern and may only be relevant to HPO and MP, so I don't mind if we don't want to keep it."

If its used, it should be a pattern IMHO!

[cmungall]

The DP should align with both GO response-to DPs and ECTO DPs @diatomsRcool, need to make sure they also align with experiment DPs, cc @bpeters42

[mbrush]

@nicolevasilevsky I forwarded you an email and files that have info about the antibody modeling work that is a component of the larger Reagent Ontology. Feel free to disseminate, and I'm happy to consult if you have questions or want feedback on your design patterns.

[nicolevasilevsky]

@matentzn would an organism be a material entity? Because the antigen could be a bacteria, virus, etc.

@mbrush thanks for sending the antibody modeling files! All - I added an image of the model to this comment below.

It would be great if we could come up with a pattern for this, it was too complicated for me, I didn't know how to do it. If someone else can take a pass, that would be great.

[pnrobinson]

Complexes like this are also often deposited somewhere, e.g., in the kidney. Can we describe the use case in English first please?

[nicolevasilevsky]

@pnrobinson this pattern is intended to be used for the children of 'increased IgE level', like 'Increased anti-animal protein IgE antibody level' and 'Increased anti-bacteria IgE antibody level'

these terms currently do not have logical definitions, but the parent 'increased IgE level' has the logical def:

'has part' some ('increased amount' and ('inheres in' some ('IgE immunoglobulin complex, circulating' and ('part of' some blood))) and ('has modifier' some abnormal))