New term request, 'has disease driver'

[lschriml]

I am requesting a new relation term to define the relationship between a disease driver and a disease. For the Human Disease Ontology project.

Definition: A relation between a material entity and a disease of a host, in which the material entity is not part of the host itself, and the condition results in pathological processes.

Aligning this definition to 'has allergic trigger'.

Thank you, Lynn Schriml

[nlharris]

Is this still needed? Who can address this?

[matentzn]

This issue is only a few days old.. @lschriml can address it when she starts working on patternisation of her driver classes, and we can help.

[lschriml]

@nlharris and @matentzn -- Yes, the term is still needed, What do you need for this RO term to be created ?

Cheers, Lynn

[matentzn]

@lschriml i think the main thing is to decide whether we can omit the disease and simply use has driver. This will make it easier to integrate with other modelling patterns.

Also remember that has driver connects the disease with the driver - not the driver with the element (like alcohol).

My preferred option: you provide all the metadata here:

• label
• definition
• orcid
• comment with intended use case
• rdfs:seeAlso to this github issue

Then we make this the first test for our new template based pipeline, which will make @cthoyt happy.

[lschriml]

Hello @matentzn: I see your point.

label: has_driver: Definition: A relation between a material entity and a disease of a host, in which the material entity is not part of the host itself, and the condition results in pathological processes.

My ORCID: 0000-0001-8910-9851

rdfs:seeAlso https://github.com/oborel/obo-relations/issues/506

[matentzn]

Werent we going for some model like that?

fetal alcohol disorder--[has driver]-->alcohol driver--[has stressor?]-->alcohol

[lschriml]

yes, I think that is the modeling you proposed and we discussed. I see how it is built so that the ontology connections make sense.

However, from an epidemiological perspective, the alcohol is the driver, I am not sure how we would define 'stressor' -- as the 'driver' is the thing that is causing the pathophysiology end result

What I really want to model is that a driver (e.g. alcohol) is 'disease driver' resulting in a disease (e.g. fetal alcohol syndrome).

[lschriml]

Thinking of modeling consistency: I was modeling the requested RO term name based on the RO term, 'has allergic trigger', where the modeling is: disease (e.g. asthma) - 'has allergic trigger' some pollen thus for disease drivers: disease -- 'has disease driver' some alcohol

[matentzn]

In this case, we need something like this:

You curate:

`fetal alcohol disorder`--[`realised in response to`]-->`alcohol driver`--[`has stimulus`]-->`alcohol` 

You can use has stimulus to be consistent with ECTO, and thedriver class takes care of the driver semantics (i.e. the fact that it is not just a stimulus).

You infer:

`fetal alcohol disorder`--[`has driver`]-->`alcohol` 

Using these axioms:

driver SubClassOf isDriver some self
`has driver` subChainOf `realised in response to` o `isDriver` o `has stimulus`

This is a bit sophisticated, @balhoff what do you think of this?

[lschriml]

Getting back to this request.

I would like to have 'has disease driver' added to the RO.

Definition: A relation between a material entity and a disease of a host, in which the material entity is not part of the host itself, and the condition results in pathological processes.

Aligning this definition to 'has allergic trigger' RO term.

Cheers, Lynn

[matentzn]

You can add the term using Protege in the appropriate place!

[lschriml]

Hello @matentzn -- I'm not sure I understand your message. I am not a RO developer. Can one of the RO developers please add this new term.

Thank you, Lynn

[matentzn]

No worries. RO is a community-edited ontology, I don't think there is an RO developer per se - we all have to do our own additions and pull requests usually.

[lschriml]

Ok. Thanks Nico. So should I go ahead and make a pull request on RO and add the RO term ?

Do you want me to add a more generic ‘has driver’ as well ?

Cheers, Lynn

On Nov 30, 2021, at 4:56 AM, Nico Matentzoglu @.***> wrote:

 No worries. RO is a community-edited ontology, I don't think there is an RO developer per se - we all have to do our own additions and pull requests usually.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub, or unsubscribe.

[matentzn]

Yes, maybe add both. Also, you first need to add yourself yo this file:

https://github.com/oborel/obo-relations/blob/master/src/ontology/ro-idranges.owl

To secure an ID range. Make a pull request and you can tag me as a reviewer and I will take care of the rest

[lschriml]

Thank you Nico !! I have created the pull request.

I am not able to select a reviewer.

Cheers, Lynn

On Wed, Dec 1, 2021 at 3:20 AM Nico Matentzoglu @.***> wrote:

Yes, maybe add both. Also, you first need to add yourself yo this file:

https://github.com/oborel/obo-relations/blob/master/src/ontology/ro-idranges.owl

To secure an ID range. Make a pull request and you can tag me as a reviewer and I will take care of the rest

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/oborel/obo-relations/issues/506#issuecomment-983398905, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DOXBDJBUAASC2K3Q5LUOXLEBANCNFSM5G72LPFQ .

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[lschriml]

@matentzn -- I have added the new terms, and initiated a pull request

[lschriml]

@cmungall @matentzn -- Looking forward to having these two new RO terms added to the next RO release. -- Requesting the final review of #531 pull request, so that these terms can be used for annotations.

Cheers, Lynn

[matentzn]

I am on leave now for quite a while - keep pinging @cmungall here to get it merged. Thanks!

[lschriml]

Thank you @matentzn -- Happy Holidays !!

@cmungall -- Chris -- please let me know if I can provide any further info to get these RO terms added.

Cheers, Lynn

[nlharris]

Closed by #531