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IDO and OBI 'pathogen role'
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.
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...(?)
For IDO perhaps construe as "... it or one of its products is [in contact with] an organism towards which it has the pathogenic disposition"
@zhengj2007 - are you in contact with the IDO group about changing the definition? @lgcowell , what is the IDO state?
@bpeters42 No. But I can help on definition changes and make a new release if @lgcowell is OK for it.
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!
Lindsay G. Cowell, MS, PhD Associate Professor Peter O’Donnell Jr. School of Public Health Department of Immunology, School of Biomedical Sciences Population Science Program, Simmons Comprehensive Cancer Center UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-9066 Office | G9.220E, MC9066 Phone | 214-648-2289 Fax | 214-648-2064 @.@.> https://www.utsouthwestern.edu/education/public-health/
From: jie zheng @.> Date: Monday, April 29, 2024 at 12:06 PM To: obi-ontology/obi @.> Cc: Lindsay Cowell @.>, Mention @.> Subject: Re: [obi-ontology/obi] IDO and OBI 'pathogen role' (Issue #1723) EXTERNAL MAIL
@bpeters42https://urldefense.com/v3/__https:/github.com/bpeters42__;!!MznTZTSvDXGV0Co!FUeDb2gPG351VR1s64EHQD8R5ER_9CAiMbt9X-G6bNsYHsuiyGepI5JDJXV2QxaekfIiKOWlQaKAFGPE_TsvtYDIrB49K0nExb2xpQ$ No. But I can help on definition changes and make a new release if @lgcowellhttps://urldefense.com/v3/__https:/github.com/lgcowell__;!!MznTZTSvDXGV0Co!FUeDb2gPG351VR1s64EHQD8R5ER_9CAiMbt9X-G6bNsYHsuiyGepI5JDJXV2QxaekfIiKOWlQaKAFGPE_TsvtYDIrB49K0mDSTz_kw$ is OK for it.
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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.
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".
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!
I think the OBI definition is circular. Very happy to see the IDO term replace the OBI term.
I also think that the definition of pathogenic disposition needs improvement: A disposition to initiate processes that result in a disorder. There are many other non-infectious processes that result in a disorder. This term needs to be refined. @lgcowell https://github.com/lgcowell @John Beverley @.> @Shane Babcock @.>
Thanks, Asiyah
On Mon, Apr 29, 2024 at 2:46 PM jie zheng @.***> wrote:
Just let me know when it's ready to update the IDO and make a new release. @lgcowell https://github.com/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!
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Pathogenic disposition is not intended to be restricted to the infectious disease context. The subtype, infectious disposition, captures those pathogenic dispositions that are specific to infectious disease.
Does that answer your concern?
Thanks,
Lindsay
Lindsay G. Cowell, MS, PhD Associate Professor Peter O’Donnell Jr. School of Public Health Department of Immunology, School of Biomedical Sciences Population Science Program, Simmons Comprehensive Cancer Center UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-9066 Office | G9.220E, MC9066 Phone | 214-648-2289 Fax | 214-648-2064 @.@.> https://www.utsouthwestern.edu/education/public-health/
From: Asiyah Yu Lin @.> Date: Monday, April 29, 2024 at 2:01 PM To: obi-ontology/obi @.> Cc: Lindsay Cowell @.>, Mention @.> Subject: Re: [obi-ontology/obi] IDO and OBI 'pathogen role' (Issue #1723) EXTERNAL MAIL I think the OBI definition is circular. Very happy to see the IDO term replace the OBI term.
I also think that the definition of pathogenic disposition needs improvement: A disposition to initiate processes that result in a disorder. There are many other non-infectious processes that result in a disorder. This term needs to be refined. @lgcowell https://github.com/lgcowellhttps://urldefense.com/v3/__https:/github.com/lgcowell*3E__;JQ!!MznTZTSvDXGV0Co!COOXFpq5-OOidpOWon5wxVbbQvvvMhIOSe-tBjlnOoRdNETJ9Ta3eZJvZTAytVp6EFf5Yze8p2cKHRPx1ddyzloH9mpYut4f2lPY-A$ @John Beverley @.> @Shane Babcock @.>
Thanks, Asiyah
On Mon, Apr 29, 2024 at 2:46 PM jie zheng @.***> wrote:
Just let me know when it's ready to update the IDO and make a new release. @lgcowell https://github.com/lgcowellhttps://urldefense.com/v3/__https:/github.com/lgcowell*3E__;JQ!!MznTZTSvDXGV0Co!COOXFpq5-OOidpOWon5wxVbbQvvvMhIOSe-tBjlnOoRdNETJ9Ta3eZJvZTAytVp6EFf5Yze8p2cKHRPx1ddyzloH9mpYut4f2lPY-A$
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!
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It does. Thank you, Lindsay.
On Tue, Apr 30, 2024 at 1:23 PM lgcowell @.***> wrote:
Pathogenic disposition is not intended to be restricted to the infectious disease context. The subtype, infectious disposition, captures those pathogenic dispositions that are specific to infectious disease.
Does that answer your concern?
Thanks,
Lindsay
Lindsay G. Cowell, MS, PhD Associate Professor Peter O’Donnell Jr. School of Public Health Department of Immunology, School of Biomedical Sciences Population Science Program, Simmons Comprehensive Cancer Center UT Southwestern Medical Center 5323 Harry Hines Blvd., Dallas, Texas 75390-9066 Office | G9.220E, MC9066 Phone | 214-648-2289 Fax | 214-648-2064 @.@.> https://www.utsouthwestern.edu/education/public-health/
From: Asiyah Yu Lin @.> Date: Monday, April 29, 2024 at 2:01 PM To: obi-ontology/obi @.> Cc: Lindsay Cowell @.>, Mention @.> Subject: Re: [obi-ontology/obi] IDO and OBI 'pathogen role' (Issue #1723) EXTERNAL MAIL I think the OBI definition is circular. Very happy to see the IDO term replace the OBI term.
I also think that the definition of pathogenic disposition needs improvement: A disposition to initiate processes that result in a disorder. There are many other non-infectious processes that result in a disorder. This term needs to be refined. @lgcowell https://github.com/lgcowell< https://urldefense.com/v3/https:/github.com/lgcowell*3E;JQ!!MznTZTSvDXGV0Co!COOXFpq5-OOidpOWon5wxVbbQvvvMhIOSe-tBjlnOoRdNETJ9Ta3eZJvZTAytVp6EFf5Yze8p2cKHRPx1ddyzloH9mpYut4f2lPY-A$> @John Beverley @.> @Shane Babcock @.>
Thanks, Asiyah
On Mon, Apr 29, 2024 at 2:46 PM jie zheng @.***> wrote:
Just let me know when it's ready to update the IDO and make a new release. @lgcowell https://github.com/lgcowell< https://urldefense.com/v3/https:/github.com/lgcowell*3E;JQ!!MznTZTSvDXGV0Co!COOXFpq5-OOidpOWon5wxVbbQvvvMhIOSe-tBjlnOoRdNETJ9Ta3eZJvZTAytVp6EFf5Yze8p2cKHRPx1ddyzloH9mpYut4f2lPY-A$>
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!
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- 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.