Re: Issue 18 in infectious-disease-ontology: infectious agent - organisms only

[infectious-di...@googlecode.com]

Comment #3 on issue 18 by bpet...@liai.org: infectious agent - organisms
only
http://code.google.com/p/infectious-disease-ontology/issues/detail?id=18

Hi Lindsay,

When we just looked into the IDO definition, both the logical and textual
still only refer to organism:
http://www.ontobee.org/browser/rdf.php?o=IDO&iri=http://purl.obolibrary.org/obo/IDO_0000596



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[infectious-di...@googlecode.com]

Updates:
Status: Started

Comment #4 on issue 18 by lindsay....@utsouthwestern.edu: infectious agent

- organisms only
http://code.google.com/p/infectious-disease-ontology/issues/detail?id=18

Hi Bjoern,

Thanks for your note. This has been one of those hotbed issues where we go
back and forth between "organism" and "material entity" to allow or
disallow the inclusion of prions (and all sorts of other things). No
matter which way we go, someone is up in arms (I'm sure you have that
experience with OBI).

For the record, when we use organism, prions are excluded, as you point
out. When we use material entity, prions are included, which some people
object to, but the primary complaint is that other kinds of things are then
also allowed, such as the tasmanian devil face "cancer".

I think excluding prions will cause more problems for users and IDO
compatibility with other resources than allowing tasmanian face cancers, so
I will put revising the relevant terms in my queue.

If anyone strongly objects let me know.

Thanks,

Lindsay

[Scheuermann, Richard]

What if you had infectious disease as a child of transmissible disease?

Sent from my iPhone

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[He, Yongqun]

I agree that prion induced disease can be considered as an infectious disease, but cancer is not. The difference is that prion comes from outside the host body, while the cancer is derived from mutation of some host cell itself.

It might help to assert an infectious disease as a child of transmissible disease, depending on how the transmissible disease is defined.

Oliver

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[infectious-di...@googlecode.com]

Comment #5 on issue 18 by alanrut...@gmail.com: infectious agent -
organisms only
http://code.google.com/p/infectious-disease-ontology/issues/detail?id=18

What's wrong with including the tasmanian devil face "cancer"?


On Mon, May 6, 2013 at 1:24 PM,
<infectious-di...@googlecode.com>wrote:

[Lindsay Cowell]

Do you mean as way to address the prion issue or address the face cancer issue?

Right now, infectious disease is defined in a way that points back to infectious agent, so altering the definition of infectious disease wouldn't affect what is considered an infectious agent. To do that, I think we need to modify the definition for infectious agent.

Thanks,

Lindsay

-------------------------------------------------------------------
Lindsay G. Cowell, PhD
Division of Biomedical Informatics
Department of Clinical Sciences
University of Texas Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.
Dallas, TX 75390-9066

F4.212b, MC9066

phone: 214-648-2289
fax: 214-648-2064
Lindsay...@utsouthwestern.edu


________________________________

UT Southwestern Medical Center
The future of medicine, today.

[Lindsay Cowell]

On May 6, 2013, at 2:48 PM, He, Yongqun wrote:

> I agree that prion induced disease can be considered as an infectious disease, but cancer is not. The difference is that prion comes from outside the host body, while the cancer is derived from mutation of some host cell itself.

In this case, the "cancer" is not host derived. That's why it causes a problem for us.

[He, Yongqun]

I see. The Tasmanian devil tumor (cancer) disease appears to pass through biting:
http://www.dpiw.tas.gov.au/inter.nsf/WebPages/LBUN-5QF86G

In this case, if we use a definition of the infectious agent based on self vs non-self, the Tasmanian devil cancer disease is considered as an infectious disease.

[Bjoern Peters]

Exactly - the Tasmanian devil tumor should not classify as an infectious disease, but not as a 'classical cancer' (but that is someone else's problem). 

There are most likely other eukaryotes out there that originated a long time ago from multicellular animials like the Tasmanian devil tumor cell line did now, and those Eukaryotes would now be uncontroversially considered infectious pathogens because their origin is no longer apparent. 

- Bjoern 

---

Bjoern Peters
Assistant Professor
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

[Scheuermann, Richard]

To me prion mediated disease is more like the cancer. They are both host derived.

Don't know why having a transmissible disease part wouldn't solve the problem, allowing us to capture the differences between host derived vs non host derived and between reproduction based on polymerization and reproduction based on post translational modification/aggregation.

Sent from my iPhone

[He, Yongqun]

I see no conflict between the two statements:

- All infectious diseases are transmissible disease.
- All infectious agents are agents that are not part of an organism (non-self) but can infect the organism.

A cancer that can be infectious or transmissible, such as the Tasmanian devil cancer disease, is due to that such cancer cells can infect other hosts. If the agent (like classic cancer) can only cause disease in self but cannot transmit to infect another host organism, it is not considered as infectious agent, so there will be no infectious disease.

It appears that there are two types of infectious agents:
- host-born infectious agent: including prion-mediated disease, the Tasmanian devil cancer disease, and others. These host-born agents will have the ability to infect other hosts.
- non-host-born infectious agent: bacterial, virus, fugal, and parasitic agents that cause infectious diseases.

[Scheuermann, Richard]

A. According to this argument, all cancer would be considered an
infectious disease. See for example:

1: Lipshutz GS, Mihara N, Wong R, Wallace WD, Allen-Auerbach M, Dorigo O,
Rao PN,
Pham PC, Pham PT. Death from metastatic donor-derived ovarian cancer in a
male
kidney transplant recipient. Am J Transplant. 2009 Feb;9(2):428-32. doi:
10.1111/j.1600-6143.2008.02507.x. PubMed PMID: 19178417.


2: Golfinopoulos V, Pentheroudakis G, Kamakari S, Metaxa-Mariatou V,
Pavlidis N.
Donor-derived breast cancer in a bone marrow transplantation recipient.
Breast
Cancer Res Treat. 2009 Jan;113(2):211-3. doi: 10.1007/s10549-008-9922-7.
Epub
2008 Feb 9. Erratum in: Breast Cancer Res Treat. 2009 Jan;113(2):215.
Golfinopouloss, Vassilis [corrected to Golfinopoulos, Vassilis]. PubMed
PMID:
18264757.


3: Bellati F, Napoletano C, Nuti M, Benedetti Panici P. Death from
metastatic
donor-derived ovarian cancer in a male kidney transplant recipient. Am J
Transplant. 2009 May;9(5):1253. doi: 10.1111/j.1600-6143.2009.02601.x.
PubMed
PMID: 19422352.


4: Loh E, Couch FJ, Hendricksen C, Farid L, Kelly PF, Acker MA,
Tomaszewski JE,
Malkowicz SB, Weber BL. Development of donor-derived prostate cancer in a
recipient following orthotopic heart transplantation. JAMA. 1997 Jan
8;277(2):133-7. PubMed PMID: 8990338.


5: Winter TC, Keller PR, Lee FT Jr, Pozniak MA. Donor-derived malignancy:
transmission of small-cell lung cancer via renal transplantation. J
Ultrasound
Med. 2001 May;20(5):559-62. PubMed PMID: 11345116.


B. Kuru, BSE and scrapie are classified as transmissible spongiform
encephalopathies, not infectious spongiform encephalopathies.

C. My proposal is that flu is an infectious disease which is a
transmissible disease. BSE is a transmissible disease, but not an
infectious disease. Cancer is a transmissible disease, but not an
infectious disease.


--------------------------------------------
Richard H. Scheuermann, Ph.D.
Director of Informatics
J. Craig Venter Institute
10355 Science Center Dr.
San Diego, CA 92121

rscheu...@jcvi.org
858-200-1876

[Sivaram Arabandi, MD]

> B. Kuru, BSE and scrapie are classified as transmissible spongiform
> encephalopathies, not infectious spongiform encephalopathies.
>
> C. My proposal is that flu is an infectious disease which is a
> transmissible disease. BSE is a transmissible disease, but not an
> infectious disease. Cancer is a transmissible disease, but not an
> infectious disease.

+1

Attached is an article "Sacred Disease of Our Times: Failure of the Infectious Disease Model of Spongiform Encephalopathy" that discusses these very aspects. Quoting from article
'Transmission of virtually every form of cancer from one human to another has been described in transplantation.15 Fortunately this is rare but the fact that donor cancers can be transmitted to transplant recipients does not cause us to treat cancer as an infectious disease. The viral etiology of some cancers is another matter.'
'Public health policy would be better served if TSE were classified with cancer as a transmissible somatic proliferative disorder. Both diseases occur sporadically, probably due to failure of surveil- lance-repair mechanisms.'

[He, Yongqun]

I agree that infectious disease is a transmissible disease. The question is what are the differences between an infectious disease and a transmissible disease. One critical point is probably the transmission route. An infectious disease, but not all transmissible disease, is able to transmit through a natural route without human intervention.

 

Classical cancers are not considered as infectious diseases. All the five examples Richard provided are due to the transplantation. The transplantation is a type of human intervention. I think an infectious agent is able to infect through a natural infectious process, not through a human intervention.  

 

Another example: In many cases, we can inject a tumor cell line into a mouse and induce cancer in the mouse. However, the tumor cell line cannot be considered as  an infectious agent. So, to differentiate a transmissible disease from an infectious disease, we may need to add that an infectious disease, caused by an infectious agent, needs to infect through its own natural route, instead of through a human intervention.

 

If we use this definition, we can say classical cancer is not an infectious disease. Some special caners may be if they can transmit through a natural infection route.

 

If BSE cannot infect/transmit by itself (without human intervention) as shown in the paper Sivaram provided, it is not considered as an infectious disease but can be classified as a non-infectious transmissible disease.

 

As I know, some prion diseases may be infectious and so can be considered as infectious disease, for example:

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Prions.html#Infectious_Prion_Diseases

However, each prion disease may need to be examined case-by-case to see if it can be transmitted by itself without human intervention.

 

Oliver

 

 

 

From: ido-d...@googlegroups.com [mailto:ido-d...@googlegroups.com] On Behalf Of Sivaram Arabandi, MD
Sent: Wednesday, May 08, 2013 9:37 AM
To: ido-d...@googlegroups.com
Subject: Re: Issue 18 in infectious-disease-ontology: infectious agent - organisms only

 

> B. Kuru, BSE and scrapie are classified as transmissible spongiform

--Sivaram

> B. Kuru, BSE and scrapie are classified as transmissible spongiform
> encephalopathies, not infectious spongiform encephalopathies.
>
> C. My proposal is that flu is an infectious disease which is a
> transmissible disease.  BSE is a transmissible disease, but not an
> infectious disease.  Cancer is a transmissible disease, but not an
> infectious disease.
>
>

[Scheuermann, Richard]

It seems that you have to make your model overcomplicated to match your definitions.  Also, if we accept the OGMS proposal the disease are dispositions, they should not be based on whether human intervention was involved.

--------------------------------------------

Richard H. Scheuermann, Ph.D.

Director of Informatics

J. Craig Venter Institute

10355 Science Center Dr.

San Diego, CA 92121

rscheu...@jcvi.org

858-200-1876

[He, Yongqun]

Yes, my model is somehow complicated. I think it more by aligning the concepts with what I have learned in biology. I accept the OGMS proposal that the disease is a disposition. However, as subclasses of disease, it is likely fine to include some extra restriction.

 

Oliver

[Lindsay Cowell]

On May 7, 2013, at 2:26 PM, Scheuermann, Richard wrote:

> To me prion mediated disease is more like the cancer. They are both host derived.
>
> Don't know why having a transmissible disease part wouldn't solve the problem, allowing us to capture the differences between host derived vs non host derived and between reproduction based on polymerization and reproduction based on post translational modification/aggregation.

This is consistent with the way IDO is currently set up. We did not add the relevant transmissible disease terms, as we assumed folks working on those diseases would do that, but we can certainly add any needed to help address this problem.

OBI folks - would this approach address your needs regarding prion?

Thanks,

Lindsay