disease course types

[Scheuermann, Richard]

I am involved in a clinical metadata working group with Chris Stoeckert that involves the NIAID funded Genome Sequencing Centers and Bioinformatics Resource Centers.  We had a discussion about the use of "symptom onset" as one of our required data fields and ended up deciding to use OGMS "disease course" instead, which prompted me to take a look at our definitions.  These are the ones I pulled out of Ontobee; not sure if they are current.

Disease course - The totality of all processes through which a given disease instance is realized.

Acute disease course - A disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset.

Chronic disease course - A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range.

Progressive disease course - A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis.

Transient disease course - A disease course that terminates in a return to normal homeostasis.

During our discussion we realized that there was a distinction between the onset of disease and the course of the disease, and that basing distinctions on the rate of onset is problematic since at one point in time the disease/disease realization/symptom does not exist and at the next point in time it does exist; "onset" pe rse is instantaneous.  We might want to talk about rapid realization/progression of a disease course.  Indeed, I think that transient, chronic and progressive disease courses can all start with an initial rapid phase.  Maybe when we use the term "onset", we are refer to an initial period of time of some sort, rather than an initiating event.  At a minimum, this would need to be clarified.

That being said, I think the definition of acute disease course is problematic.  If you were to poll relevant stakeholder, including clinicians, I expect that any examples of acute disease would be consistent with our definition of transient disease course.  

Thus I would propose the following:

1. The current acute disease course should be removed.
2. Acute disease course should be listed as a synonym to transient disease course with the current definition of transient disease course used.
3. That we add a new term "disease course part" as a sibling of disease course, that could be defined as - a temporal stage of a disease course.
4. That we add a new term "disease course onset" which would be a child of disease course part, that could be defined as – the initial stage of a disease course.  (Convalescence could be another type of disease course part.)
5. That "acute disease onset" be added as a child of disease course onset, defined as – a disease onset in which signs and symptoms progress relatively rapidly in comparison with a canonical disease course.

Cheers,

Richard

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

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

[Scheuermann, Richard]

Lynn Schriml is also part of the group

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

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

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[Bill Hogan]

Richard,

The definitions you list certainly lead to problems, as you point out: a disease course could be an instance of both acute disease course and chronic disease course (had a rapid onset but then was typically chronic after that).  

What part is the "onset" however?  I would argue that we are usually talking about the clinical onset (as opposed to the pre-clinical part of the course that comes before it).  Admittedly, the current definitions are vague on this point, too.

Also, although BFO 2.0 is still evolving w.r.t. "properties" of processes, whether the onset was rapid or slow seems to be what currently is called a process profile.  So it would be an onset that exemplifies a particular pattern in time.

But generally, I am in favor of the proposed changes.

Bill

Bill

[Albert Goldfain]

I have created an issue on the ogms tracker for this topic:
https://code.google.com/p/ogms/issues/detail?id=80

Barry, can you please place 'disease course subtyping' on the agenda for the ICBO OGMS workshop:
http://ncorwiki.buffalo.edu/index.php/OGMS_Workshop

I don't have much intuition as to how these subtypes are used clinically, but regarding the profile of the disease course (read: the way a disease manifestation can unfold) it seems to be relative to some reference...but it might be quite challenging to spell out what this reference really is.  For example, taking the term SARS at face value Severe *ACUTE* Respiratory Syndrome...is probably rapid onset relative to other respiratory diseases, not an acute version of a non-acute disease course.

AG

[Bill Hogan]

With respect to the reference problem, it also exists for rapid heart beat, tachycardia, tachypnea, bradycardia, etc.

Yes, diseases with 'acute' in their name are generally types of disease without a chronic counterpart, with some exceptions, and in the exceptions I can think of right now, there are really acute and chronic phases of the disease course of a single disease:

Hepatitis B: most individuals just have an acute phase that resolves, but some individuals have the acute phase followed by long-term chronic infection.  These two cases are NOT considered subtypes of Hep B infection, per my clinical experience.

HIV: can present with acute phase that presents with lymphadenopathy, fatigue, malaise, etc. before chronic infection

The acute "part" of these diseases are typical, not atypically short presentations of something else.

Bill

[Scheuermann, Richard]

Defining the reference is indeed challenging, but it would be what is considered to be clinically normal given an individual patients context (age, race, gender, underlying conditions, etc.).

Richard

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

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

[Scheuermann, Richard]

As an alternative, we could have acute disease course as a child of transient disease course, defined as a transient disease course with an acute disease onset.

Richard

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

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

From: <Scheuermann>, "Richard H. Scheuermann" <rscheu...@jcvi.org>
Date: Thursday, May 16, 2013 12:21 PM
To: "ogms-d...@googlegroups.com" <ogms-d...@googlegroups.com>
Subject: disease course types

[Peter Robinson]

Hi Richard,

your suggestions sound reasonable, but I am not so sure it is a good idea to rely upon the existence of "typical" or "canonical" disease courses. It would be quite difficult to define this in a way that is computable, and it seems to me that "acute" should be defined purely on the basis of temporal aspects. There are diseases that are always "acute", so that the clause "progress relatively rapidly in comparison with a canonical disease course." would mean that this group of acute onset diseases would not be identified as acute by your definition.

-Peter

[Prabhu Shankar]

I just want to add that we also have 'sub-acute' 'onset' as well as 'acute - on - chronic' 'disease course' illnesses. Some examples in medical literature are sub-acute combined degeneration and many chronic glomerulonephritedes (acute - on - chronic). I also think these categorizations are all based on temporal aspects.

--
“Superior doctors prevent the disease. Mediocre doctors treat the disease before evident. Inferior doctors treat the full-blown disease.” -Huang Dee Nai-Chan 2600 BC; 1st Chinese Medical Text.

[Barry Smith]

On Mon, May 20, 2013 at 9:17 AM, Albert Goldfain <albertg...@gmail.com> wrote:

I have created an issue on the ogms tracker for this topic:
https://code.google.com/p/ogms/issues/detail?id=80

 

Barry, can you please place 'disease course subtyping' on the agenda for the ICBO OGMS workshop:
http://ncorwiki.buffalo.edu/index.php/OGMS_Workshop

Done

I made this a subtopic of "BFO 2.0 and Process Patterns" in the schedule. This reflects the fact that we are now working under the assumption that BFO 2.0 will include the term 'process pattern' and the documentation is in process of being amended accordingly.

Examples of process patterns are: cyclical process, beating process, 2 beat per minute beating process, and so on. 

If a phase b of a disease course is acute, then we say 

phase b has acute process pattern

If a later phase c is chronic, then we say

phase c has chronic process pattern

If the whole disease course begins as acute and ends as chronic we say 

the whole process (= b+c = b followed by c) has acute-followed-by-chronic process pattern

I don't have much intuition as to how these subtypes are used clinically, but regarding the profile of the disease course (read: the way a disease manifestation can unfold) it seems to be relative to some reference...but it might be quite challenging to spell out what this reference really is.  For example, taking the term SARS at face value Severe *ACUTE* Respiratory Syndrome...is probably rapid onset relative to other respiratory diseases, not an acute version of a non-acute disease course.

Some process patterns will be relative process patterns. We hope to document this also. 

Regarding the use of 'phase' in the above -- I believe that both 'phase' and 'stage' have attractions for referring to the temporal parts of  processes which is at issue here. GO seems to be converging on 'phase'; but still uses 'stage' for a dozen or so terms; the Plant Ontology has used 'stage'. Comments on this topic, too, are welcome. BFO 2.0 officially uses 'temporal part', but we could replace this by 'phase' or 'stage' if people want this.

BS 

[Barry Smith]

On Thu, May 16, 2013 at 3:21 PM, Scheuermann, Richard <RScheu...@jcvi.org> wrote:

I am involved in a clinical metadata working group with Chris Stoeckert that involves the NIAID funded Genome Sequencing Centers and Bioinformatics Resource Centers.  We had a discussion about the use of "symptom onset" as one of our required data fields and ended up deciding to use OGMS "disease course" instead, which prompted me to take a look at our definitions.  These are the ones I pulled out of Ontobee; not sure if they are current.

Disease course - The totality of all processes through which a given disease instance is realized.

Acute disease course - A disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset.

Chronic disease course - A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range.

Progressive disease course - A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis.

Transient disease course - A disease course that terminates in a return to normal homeostasis.

During our discussion we realized that there was a distinction between the onset of disease and the course of the disease, and that basing distinctions on the rate of onset is problematic since at one point in time the disease/disease realization/symptom does not exist and at the next point in time it does exist; "onset" pe rse is instantaneous.  We might want to talk about rapid realization/progression of a disease course.  Indeed, I think that transient, chronic and progressive disease courses can all start with an initial rapid phase.  Maybe when we use the term "onset", we are refer to an initial period of time of some sort, rather than an initiating event.  At a minimum, this would need to be clarified.

That being said, I think the definition of acute disease course is problematic.  If you were to poll relevant stakeholder, including clinicians, I expect that any examples of acute disease would be consistent with our definition of transient disease course.  

Thus I would propose the following:

1. The current acute disease course should be removed.

Agreed 

1. Acute disease course should be listed as a synonym to transient disease course with the current definition of transient disease course used.

Agreed 

1. That we add a new term "disease course part" as a sibling of disease course, that could be defined as - a temporal stage of a disease course.

In BFO this should be disease course temporal part, which is a bit ugly; thus I would propose 'discourse course phase' or 'disease course stage' (see my previous email responding t oAlbert) 

1. That we add a new term "disease course onset" which would be a child of disease course part, that could be defined as – the initial stage of a disease course.  (Convalescence could be another type of disease course part.)

Agreed

 

1. That "acute disease onset" be added as a child of disease course onset, defined as – a disease onset in which signs and symptoms progress relatively rapidly in comparison with a canonical disease course.

Also agreed.

BS

 

Cheers,

Richard

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

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

[Barry Smith]

On Sat, Jun 15, 2013 at 8:32 AM, Peter Robinson <pete...@gmail.com> wrote:

Hi Richard,

your suggestions sound reasonable, but I am not so sure it is a good idea to rely upon the existence of "typical" or "canonical" disease courses. It would be quite difficult to define this in a way that is computable, and it seems to me that "acute" should be defined purely on the basis of temporal aspects. There are diseases that are always "acute", so that the clause "progress relatively rapidly in comparison with a canonical disease course." would mean that this group of acute onset diseases would not be identified as acute by your definition.

I believe that Peter's worry here is resolved by recommending use of 'transient disease course' rather than 'acute disease course'

BS 

[Sivaram Arabandi, MD]

'Transient disease course' implies a temporariness to the disease process i.e. it is short lived (e.g. Rotavirus diarrhea). 

'Acute disease course' on the other hand can be 'transient' and resolve e.g.: Acute Pancreatitis

or can be short lived and lead to death e.g.: Acute Pancreatitis

        or evolve into a 'Chronic disease course' i.e. Acute Pancreatitis leading to Chronic Pancreatitis. 

Some disorders are chronic but have acute phases (e.g. TIA (acute) in Atherosclerosis (chronic)). 

So, I don't think that the definition of 'Transient' will work for 'Acute'.

cheers

Sivaram

[Scheuermann, Richard]

Here is an extension of my initial proposal.  I tried to incorporate some of the comments in this email stream and added a couple of new concepts.  Note that this is about defining types and parts of disease courses; it is not intended as a classification of diseases.

Cheers,

Richard

1.     Disease course phase – a temporal part of a disease course

1.1.  Disease course onset – the initial phase of the disease course

1.1.1.     Acute onset - a disease course onset in which signs and symptoms progress relatively rapidly in comparison with other disease courses of similar type

1.1.2.     Insidious onset - a disease course onset in which signs and symptoms progress relatively slowly in comparison with other disease courses of similar type

1.2.  Terminal disease course phase – the final phase of a disease course

1.2.1.     Cure – the terminal phase of a disease course in which the underlying disorder has been eliminated

1.2.2.     Death by disease - the terminal phase of a disease course in which the organism is no longer considered to be alive caused in part by the disease

2.     Disease course - The totality of all processes through which a given disease instance is realized.

2.1.  Chronic disease course - A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within an abnormal homeostatic range.

2.1.1.     Chronic disease course with acute onset – a chronic disease course with an acute disease onset. (inferred)

2.1.2.     Chronic disease course with insidious onset – a chronic disease course with an insidious disease onset. (inferred)

2.2.  Transient disease course - A disease course that terminates in a return to normal homeostasis.

2.2.1.     Transient disease course with acute onset – a transient disease course with an acute disease onset. (inferred)

2.2.2.     Transient disease course with insidious onset – a transient disease course with an insidious disease onset. (inferred)

2.3.  Progressive disease course - A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis.

2.3.1.     Progressive disease course with acute onset – a progressive disease course with an acute disease onset (inferred)

2.3.2.     Progressive disease course with insidious onset – a progressive disease course with an insidious disease onset (inferred)

2.3.3.     Fatal disease course – A progressive disease course that terminates in the death of the organism caused in part by the disease.

2.3.3.1.         Fatal disease course with acute onset – a fatal disease course with an acute disease onset. (inferred)

2.3.3.2.         Fatal disease course with insidious onset – a fatal disease course with an insidious disease onset. (inferred)

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

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

From: Barry Smith <phis...@buffalo.edu>
Reply-To: "ogms-d...@googlegroups.com" <ogms-d...@googlegroups.com>
Date: Saturday, June 15, 2013 10:38 AM
To: "ogms-d...@googlegroups.com" <ogms-d...@googlegroups.com>
Subject: Re: disease course types

[Barry Smith]

THis looks good. Might it best be packaged as a module (Disease Course Ontology?) extending OGMS, rather than as part of OGMS itself.

See minor comments inline below.

On Wed, Jun 26, 2013 at 12:14 PM, Scheuermann, Richard <RScheu...@jcvi.org> wrote:

Here is an extension of my initial proposal.  I tried to incorporate some of the comments in this email stream and added a couple of new concepts.  Note that this is about defining types and parts of disease courses; it is not intended as a classification of diseases.

Cheers,

Richard

1.     Disease course phase – a temporal part of a disease course

1.1.  Disease course onset – the initial phase of the disease course

1.1.1.     Acute onset - a disease course onset in which signs and symptoms progress relatively rapidly in comparison with other disease courses of similar type

1.1.2.     Insidious onset - a disease course onset in which signs and symptoms progress relatively slowly in comparison with other disease courses of similar type 

1.2.  Terminal disease course phase – the final phase of a disease course

1.2.1.     Cure – the terminal phase of a disease course in which the underlying disorder has been eliminated

There is another (better?) sense of 'cure' as in 'the cure was to take 12 tablets a day for 3 weeks'. 

What you seem to be defining here is 'terminal phase of response to successful treatment'

1.2.2.     Death by disease - the terminal phase of a disease course in which the organism is no longer considered to be alive caused in part by the disease

why go all epistemological suddenly with this 'considered to be'?

ontologically, death by disease would just be: the terminal phase of a disease course in which death is caused by the disease

[Scheuermann, Richard]

See responses inline below

I think we can also add as a child of chronic disease course, "relapsing-remitting disease course" - a chronic disease course in which multiple cycles of worsening and improving signs and symptoms of disease occur.

Richard

From: Barry Smith <phis...@buffalo.edu>
Reply-To: "ogms-d...@googlegroups.com" <ogms-d...@googlegroups.com>
Date: Thursday, June 27, 2013 8:28 AM
To: "ogms-d...@googlegroups.com" <ogms-d...@googlegroups.com>
Subject: Re: disease course types

THis looks good. Might it best be packaged as a module (Disease Course Ontology?) extending OGMS, rather than as part of OGMS itself.

See minor comments inline below.

On Wed, Jun 26, 2013 at 12:14 PM, Scheuermann, Richard <RScheu...@jcvi.org> wrote:

Here is an extension of my initial proposal.  I tried to incorporate some of the comments in this email stream and added a couple of new concepts.  Note that this is about defining types and parts of disease courses; it is not intended as a classification of diseases.

Cheers,

Richard

1.     Disease course phase – a temporal part of a disease course

1.1.  Disease course onset – the initial phase of the disease course

1.1.1.     Acute onset - a disease course onset in which signs and symptoms progress relatively rapidly in comparison with other disease courses of similar type

1.1.2.     Insidious onset - a disease course onset in which signs and symptoms progress relatively slowly in comparison with other disease courses of similar type 

1.2.  Terminal disease course phase – the final phase of a disease course

1.2.1.     Cure – the terminal phase of a disease course in which the underlying disorder has been eliminated

There is another (better?) sense of 'cure' as in 'the cure was to take 12 tablets a day for 3 weeks'. 

What you seem to be defining here is 'terminal phase of response to successful treatment'

This cure can also happen in the absence of treatment due to, for example, an effective immune response.  Wouldn't mind a better term though.

1.2.2.     Death by disease - the terminal phase of a disease course in which the organism is no longer considered to be alive caused in part by the disease

why go all epistemological suddenly with this 'considered to be'?

ontologically, death by disease would just be: the terminal phase of a disease course in which death is caused by the disease

Ooopps.  I agree with the revised definition.

[Alexander Cox]

I suspect that the use of 'terminal' in 'terminal disease course phase' will prove confusing for many users due to the currently popular meaning of 'terminal illness' as "a disease that cannot be cured or adequately treated and that is reasonably expected to result in the death of the patient within a short period of time" (as per Wikipedia).  This definition is closer to, but not the same as, the proposed 'fatal disease course'.

At least 'fatal disease course' and 'transient disease course' should also be inferred classes.  'fatal disease course' is a disease course with terminal disease course phase 'death by disease'.   Similarly, 'transient disease course' is a disease course with terminal disease course phase 'return to homeostasis' (or whatever the appropriate phase term should be).