Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

IDO and OBI 'pathogen role' #1723

Open
zhengj2007 opened this issue Aug 23, 2023 · 37 comments
Open

IDO and OBI 'pathogen role' #1723

zhengj2007 opened this issue Aug 23, 2023 · 37 comments
Assignees
@ddooley

Comments

@zhengj2007
Copy link
Contributor

Both IDO and OBI have term 'pathogen role'. However, the term was defined slightly different.
OBI: pathogen role: Pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role

IDO: pathogen role: A role borne by pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
pathogenic disposition: A disposition to initiate processes that result in a disorder.

If they refer to same thing, I think OBI is better to replace OBI one with IDO one.
@DanBerrios
Copy link
Contributor

Discussed on OBI call: Can IDO provide justification for the wording of its definition? Why include "sufficiently close" (internal infectious disease-producing agents are necessarily "close"), and also repeat "pathogenic disposition". Perhaps "realization of pathology" is what was intended...(?)

@ddooley
Copy link
Contributor

ddooley commented Oct 30, 2023

For IDO perhaps construe as "... it or one of its products is [in contact with] an organism towards which it has the pathogenic disposition"

@bpeters42
Copy link
Contributor

@zhengj2007 - are you in contact with the IDO group about changing the definition? @lgcowell , what is the IDO state?

@zhengj2007
Copy link
Contributor Author

@bpeters42 No. But I can help on definition changes and make a new release if @lgcowell is OK for it.

@lgcowell
Copy link

lgcowell commented Apr 29, 2024 via email

@lgcowell
Copy link

lgcowell commented Apr 29, 2024 •
edited
Loading

Discussed on OBI call: Can IDO provide justification for the wording of its definition? Why include "sufficiently close" (internal infectious disease-producing agents are necessarily "close"), and also repeat "pathogenic disposition". Perhaps "realization of pathology" is what was intended...(?)

If I remember correctly, the sufficiently close was to capture situations such as diseases caused by bacterial toxins. This is a general pathogen role, not just the role for pathogens that are internal.

realization of a pathogenic disposition is, I suppose, the realization of a pathology, but we are referring to the specific pathogenic disposition borne by the same material entity that is bearer of the pathogen role being defined and towards the specific host.

Happy to discuss in a call if that is helpful.

@lgcowell
Copy link

For IDO perhaps construe as "... it or one of its products is [in contact with] an organism towards which it has the pathogenic disposition"

I think 'in contact with" could accomplish the same thing we intended with "sufficiently close".

@zhengj2007
Copy link
Contributor Author

Just let me know when it's ready to update the IDO and make a new release. @lgcowell

Jie, if you could, that would be very helpful. And I am happy to have a call to discuss the definition, and to arrange a call with John and Shane to discuss. Thanks!

@linikujp
Copy link

linikujp commented Apr 29, 2024 via email

@lgcowell
Copy link

lgcowell commented Apr 30, 2024 via email

@linikujp
Copy link

linikujp commented Apr 30, 2024 via email

@bpeters42
Copy link
Contributor

  • We are all in favor of having IDO define 'pathogen role' rather than OBI but only if it doesn't make things a lot worse in OBI
  • OBI's definition is certainly not circular, but rather spells out what organism is bearing what role in a 'causing disease' process of host and pathogen.
  • IDO definition starts with: "A role borne by pathogen" so it is not clear if is restricted to organisms. Is asbestos a pathogen? According to IDO it seems so, as pathogen is defined as: "a material with a pathogenic disposition".

Google (and the Oxford Dictionary) says: A pathogen is: "a bacterium, virus, or other microorganism that can cause disease"
There should be some resemblance of that in the definition.

@bpeters42
Copy link
Contributor

@lgcowell , is there a chance that IDO will respond to this?

@ddooley
Copy link
Contributor

ddooley commented Sep 9, 2024

@zhengj2007 @lgcowell Can you clarify in IDO what scope of "pathogen" is? It does not seem to be axiomatized as a kind of organism incl. virus in IDO?

@ddooley ddooley self-assigned this Sep 9, 2024
@lgcowell
Copy link

lgcowell commented Sep 9, 2024 via email

@lgcowell
Copy link

lgcowell commented Sep 9, 2024 via email

@zhengj2007
Copy link
Contributor Author

@lgcowell Yes. I am waiting for what the IDO:pathogen role needs to be changed. When I know, I can update the IDO and make release.

@lgcowell
Copy link

Sorry for the length, but I wanted to provide enough information so we can decide the best edits and whether to IDO or OBI definitions.

Originally, IDO had natural language definitions, axioms expressed in natural language, formal definitions that captured (or tried to capture) the logic, and then clarifying comments.

The primary term in IDO is pathogenic disposition:

  • natural language definition: A disposition to initiate processes that result in a disorder.
  • formal definition: A disposition that inheres in an object (x) relative to an organism of type Y by virtue of the fact that x has the capability to initiate processes that result in the presence of a disorder (OGMS:0000045) in organisms of type Y. If x is an organism, x is not of type Y. The disposition is realized in the processes that create the disorder.

Infectious disposition is a subtype, as mentioned earlier in this thread.

The natural language definition for pathogen is "A material entity with a pathogenic disposition." So this is not restricted to organisms. There were many debates about whether to use organism or material entity. The complications are viruses, prions, transmissible cancers, natural language usage of "pathogen" in some contexts to mean a specific causative agent of disease (not just infectious disease), and natural language usage of "pathogenic" to mean causing or capable of causing disease. Pathogenic is used more often than pathogen in contexts other than infectious disease. We ended up deciding that the definition that would be correct in the most contexts would be to use material entity rather than organism in the definition of pathogen, and to Bjoern's point, yes asbestos would be a pathogen under IDO's definition.

Infectious disposition is a subtype of pathogenic disposition which inheres in an organism and infectious agent is a suptype of organism, so the generality of non-organismal material entities is only at the level of pathogen.

For us in the infectious disease context, we are accustomed to using pathogen as a synonym for infectious agent. However, if we define pathogen and/or pathogenic disposition that narrowly, I am afraid we will end up with conflicts in other areas of biomedicine where pathogenic and (to a lesser extent) pathogen are used more generally.

Regarding the role definitions, I think the BFO definition of role has changed in the years since IDO defined its role terms, but we defined IDO roles as roles inhering in material entities participating in processes that realize both the roles and the dispositions.

The BFO role definition at the time: A role is a realizable entity which exists because the bearer is in some special physical, social, or institutional set of circumstances in which the bearer does not have to be, and is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed.

For the pathogen and infectious disease cases, we focused on the physical.

Pathogen role:

  • natural language definition: A role borne by a pathogen in virtue of the fact that it or one of its products is sufficiently close to an organism towards which it has the pathogenic disposition to allow realization of the pathogenic disposition.
  • formal definition: A role borne by an organism (x) by virtue of the fact that it has the pathogenic disposition relative to organisms of type Y, and 2) x, one of its parts, or one of its products and an organism (y) of type Y have spatiotemporal locations which allow processes resulting in disease or death of y to occur. The role is realized in y's disease course.

This is where "sufficiently close" comes in to account for the need for physical contact. The location specification also helps account for commensals that can cause disease (e.g., Staph aureus) depending on their location (on the skin or nasal mucosa versus in the blood, etc).

the other question from above is repetition of pathogenic disposition. This was just to capture that the disposition being relied is the same one inhering in the bearer of the role.

I hope I answered all the questions? Perhaps we should have a call to discuss next steps?

Thank you,

Lindsay

@lgcowell
Copy link

lgcowell commented Sep 10, 2024 via email

@lgcowell
Copy link

Note from the BFO role definition, the role can cease to exist without physical changes to the bearer, but this is not true for dispositions. So flu on a doorknob bears the relevant dispositions but not the role. After someone touches the doorknob and rubs their eye (oops), then the role is instantiated.

Or at least that was our thinking at the time. I know BFO made substantial revisions to their definition and understanding of roles, so we may need to make definition revisions to account for that.

@bpeters42
Copy link
Contributor

bpeters42 commented Sep 11, 2024 via email

@lgcowell
Copy link

lgcowell commented Sep 19, 2024 via email

@bpeters42
Copy link
Contributor

bpeters42 commented Sep 19, 2024 via email

@ddooley
Copy link
Contributor

ddooley commented Nov 19, 2024

@lgcowell @bpeters42 am I capturing new finalized definition tweaks of "IDO:pathogen role"?:

A role borne by pathogen pathogenic material entity in virtue of the fact that it or one of its products is sufficiently close to in contact with an organism towards which it has the pathogenic disposition to allow realization of the pathogenic that disposition.

I tweaked "the pathogenic" to be "that" to cue comprehension a little bit more.
I presume the pathogen role still stands as an externally grounded (in the host) disposition.
I'm motivated to use the "in contact with" phrase simply because it may avoid the ambiguity of defining "sufficiently".

@lgcowell
Copy link

lgcowell commented Nov 19, 2024 via email

@zhengj2007
Copy link
Contributor Author

So, we need to modify the definition of 'IDO:pathogen role' in IDO as:
A role borne by pathogenic material entity in virtue of the fact that it or one of its products is in contact with an organism towards which it has the pathogenic disposition to allow realization of that disposition.

@lgcowell Do you want me to update the definition and make a new IDO release?

@lgcowell
Copy link

lgcowell commented Nov 19, 2024 via email

@zhengj2007
Copy link
Contributor Author

OK. I will work on it and let you review before making the release out.

@bpeters42
Copy link
Contributor

bpeters42 commented Nov 19, 2024 via email

@zhengj2007
Copy link
Contributor Author

Current IDO:pathogen is:
A material entity with a pathogenic disposition.

@bpeters42
Do you want to change definition of 'pathogen' to:
An organism with 'pathogenic material role'.

I cannot find the term 'pathogenic material role'. Do you mean IDO:pathogen role? If so, we need to relabel it as 'pathogenic material role' or add it as an alternative label.

Besides, there is no ontology term 'pathogenic material entity'. How are we going to define it? A material entity with a 'pathogenic material role'? It is cyclical.

@lgcowell
Copy link

lgcowell commented Nov 19, 2024 via email

@bpeters42
Copy link
Contributor

bpeters42 commented Nov 23, 2024 via email

@lgcowell
Copy link

lgcowell commented Nov 24, 2024 via email

@bpeters42
Copy link
Contributor

bpeters42 commented Nov 24, 2024 via email

@lgcowell
Copy link

lgcowell commented Nov 25, 2024 via email

@bpeters42
Copy link
Contributor

Sorry, but there are downstream effects of this like pointed out in the thread above. 'pathogen role' for example refers to pathogen (see @ddooley post). And there is a question if you want to change the term definition of pathogen (which means you should have a different ID), or change the label and create a new separate term of 'pathogen' as a child of 'pathogenic material' like I suggested.

I don't want to be complicated, but we should do any such changes at once before OBI / COB adopts this.

@lgcowell
Copy link

lgcowell commented Nov 25, 2024 via email

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@ddooley ddooley

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
6 participants
@DanBerrios @ddooley @lgcowell @zhengj2007 @linikujp @bpeters42