SNOMED CT Templates

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Statusfor Review
Version

1.0

Descriptions:

Termdescription typeLanguage/acceptabilityLanguage/acceptabilityCase significance
[course] [periods of life] [morphology] of [body structure] caused by [agent] (disorder)FSNus:Pgb:Pci

[course] [periods of life] [morphology] of [body structure] caused by [agent]

SYNus:Pgb:Pci


Concept model:

Attribute

Cardinality

AttributeValueRole Group Cardinality
1..1

116680003 |Is a (attribute)|

64572001 |Disease (disorder)|



N/A

0..1

263502005 |Clinical course (attribute)|


<   288524001 |Courses (qualifier value)|


0..1

0..1

246454002 |Occurrence (attribute)|  

<  282032007 |Periods of life (qualifier value)|



1..*

@rolegroup

1..1

116676008 |Associated morphology (attribute)|

<<  409774005 |Inflammatory morphology (morphologic abnormality)|

0..1


370135005 |Pathological process (attribute)|


<<  769247005 |Abnormal immune process (qualifier value)|  OR <<  472963003 |Hypersensitivity process (qualifier value)|

0..1

363698007 |Finding site (attribute)|

< 123037004 |Body structure (body structure)|

0..1

246075003 |Causative agent (attribute)|

[agent] <   105590001 |Substance (substance)| OR <   78621006 |Physical force (physical force)|

OR <   260787004 |Physical object (physical object)|


Definition status:  


900000000000073002 |Defined|

Applies To:

<<  128139000 |Inflammatory disorder (disorder)|  

Template Language:

64572001 |Disease (disorder)|:  [[~0..1]] { [[~0..1]] 263502005 |Clinical course (attribute)| = [[+id( <288524001 |Courses (qualifier value)|) @course]] } , [[~1..*]] { [[~0..1]] 246454002 |Occurrence (attribute)| = [[+id( <282032007 |Periods of life (qualifier value)|) @life ]] , [[~1..1]] 116676008 |Associated morphology (attribute)| = [[+id( << 409774005 |Inflammatory morphology (morphologic abnormality)| ) @morphology ]], [[~0..1]] 370135005 |Pathological process (attribute)| = [[+id( << 769247005 |Abnormal immune process (qualifier value)| OR << 472963003 |Hypersensitivity process (qualifier value)| )@path]] , [[~0..1]] 363698007 |Finding site (attribute)| = [[+id( < 123037004 |Body structure (body structure)|) @site ]], [[~0..1]] 246075003 |Causative agent (attribute)| = [[+id( < 105590001 |Substance (substance)| OR < 78621006 |Physical force (physical force)| OR < 260787004 |Physical object (physical object)| ) @agent ]] }

Rules for description generation:

  1. Apply General rules for generating descriptions for templates
  2. Apply Enhancements for the Template Language
  3. Remove word 'chronic' from the descriptions of [morphology] to avoid double 'chronic', e.g. chronic chronic inflammation in descriptions. 
  4. When clinical course is chronic and morphology has value of Chronic inflammatory morphology, descriptions are commonly presented in form of -itis, e.g. Chronic hepatitis, Chronic pancreatitis. The variable [morphology] should be kept in descriptions. Then, authors should modify descriptions manually.  New rules can be developed in future to generated descriptions based on finding site, e.g. liver structure - hepatitis, pancreatic structure - pancreatitis.  

26 Comments

  1. Monica Harry

    Peter G. Williams - I discussed with Jim as per our call today and this template at this time is good to go. Do you need to run a new query or can I go ahead and review the existing results? thanks, Monica

  2. Peter G. Williams

    With Jim's advice to group "Occurrence", I'd like to make that change to the template file (the copy held by the script) and re-run.  However, I also think we might get more mileage (ie have fewer problems for you to look at) if we do the Group 1 remodelling first and then run the script to look for mismatched concepts, so I've scheduled that for tomorrow.   I'll again start with a single task until we have some confidence in the process.   Thanks!  Peter

  3. Monica Harry

    Monica Harry - I am looking at them now... 

  4. Monica Harry

    Peter G. Williams - ended up with 26 concepts in the task. Had it reviewed and have promoted. Trust that was the correct thing to do...

  5. Peter G. Williams

    Well if you were happy enough with the behaviour of the script to pass the review and promote the changes then that's great news!   And yes promoting is the right thing to do because I always write my scripts to be re-runnable and they should only change things that need changing.   So those 26 concepts should now show up as not needing any change and won't be touched again by this particular script.  

    Will you also promote the project to MAIN at some point?

  6. Monica Harry

    Sorry, should have been more explicit, it was promoted to main last night. I think the script is fantastic! thanks...

  7. Peter G. Williams

    It was agreed that we should only have an infectious pathological process where we also have an organism for a causative agent.   The template format doesn't lend itself easily to that sort of cross-field rule, so I've removed the Pathological Process for this template (and said it should only match non-organism causative agents).    I've also created Infectious inflammation of [body structure] (disorder) - In progress  which DOES have a pathological process, and specifies an organism as the causative agent.   In that case, those attributes are mandatory.

    FYI Monica Harry Yongsheng Gao

  8. Monica Harry

    Yongsheng Gao - this template is ready for review please. thanks, Monica

  9. Yongsheng Gao

    Monica Harry Peter G. Williams  Causative agent should be more specific, e.g. |Substance| or |Physical force|. This would exclude |Organism| for infectious disorders. Chronic infectious disorder with inflammation have already been covered by templates for infectious diseases. 

    FSN and synonym should include all possible variables, e.g. Chronic [period of life] [morphology] of [body structure] caused by [agent]. The template should only allow a single role group. Role group cardinality should be changed from [1..*] to [1..1]. 

    I have updated rules for descriptions by referring to the general rules. So, we can have consistent approach for all templates. We also need a specific rule to avoid double 'chronic' in descriptions, 'chronic' from clinical course and chronic morphologies. The issue for morphologies with word 'chronic' could be addressed in future (out of scope for this project).

       

    1. Monica Harry

      This could be used for either Acute or chronic inflammatory disorders now?

      1. Yongsheng Gao

        I agree that this template can be generalised for inflammatory disorders regardless acute or chronic. I have made further changes to domain and cardinality. If it is fine with you, I will make it ready for implementation. Cheers, Yong

        1. Monica Harry

          Great, thank you. One Q: what is the significance of the single "<" vs double "<<" - is the template correct ie. where I put "<"? 

      2. Peter G. Williams

        In that case we'll need to add organism back in as a causative agent?  I've got 3195 misaligned concepts right now!   Trying again allowing for organisms...

        Also allowing for optional pathological process.  I see from the comments above that I hit this before in November last year.   I'll run two templates - adding the one for the organisms with an infectious process.   Oh, I see that template was removed.

        Will we add these two in as optional and make this template work for the infectious case also?

  10. Peter G. Williams

    Monica Harry Clinical course is not optional in this template?

    1. Jim Case

      It should be...

  11. Yongsheng Gao

    I have updated the cardinality and finding site as optional and restrict their ranges as well. There could be repeating role groups for inflammation of multiple sites, e.g. bilateral.

  12. Peter G. Williams

    Since we have the template for Infectious inflammation of body structure, I think I'm OK to remove the pathological process from this template Monica Harry?  We're not allowing an organism for a causative agent here.

  13. Monica Harry

    Peter G. Williams Seems to make sense.

  14. Penny Livesay

    Since the clinical course has a cardinality of 0..1, it is not obligatory to include it in the definition of an inflammatory disorder.  However, I think explicit guidance is needed on whether all concepts with an associated morphology of Chronic inflammatory morphology (or one of its subtypes) should be modeled with a Clinical course Chronic course, and conversely, should all inflammatory disorder concepts modeled with a Clinical course Chronic course also be given an associated morphology of Chronic inflammatory morphology?  The same questions would apply to acute inflammatory disorders - do the clinical course and the inflammatory morphology always match?  

    I think explicit guidance is needed on these points as it's not yet clear whether only one of the following approaches is correct, or, if more than one may be correct, how authors should determine which is appropriate in a given case:

    • a clinical course + an acute or chronic inflammatory morphology
    • a clinical course + inflammatory morphology (not specified as acute or chronic)

    • an acute or chronic inflammatory morphology and no clinical course

    1. Monica Harry

      Thanks Penny, I will discuss with editorial panel team but think this belongs in the Ed. guide rather than on this page here. thanks, Monica

    2. Jim Case

      Penny Livesay , the difference here is that in the inflammatory morphology, what is "meant" by acute and chronic is the actual types of cell infiltration (neutrophils vs. lymphocytes/monocytes).  While a chronic inflammatory response may take longer than an acute inflammatory response, the clinical course is mean to imply the specific temporal aspects as opposed to the morphology...

      1. Penny Livesay

        Hi Jim,

        Understood re the inflammatory morphology - the question is whether we can provide editorial guidance to aid accurate, consistent modeling of disorders involving inflammation, since the clinical course attribute is optional in the template.  I agree with Monica's comment that this information would likely fit better in the Editorial Guide, perhaps as additional content in the coverage of inflammatory disorders in the Specific Disorders section.

        1. Jim Case

          Agree, editorial guidance would be best.

  15. Penni Hernandez

    Yongsheng Gao Peter G. Williams

    246075003 |Causative agent (attribute)| needs the range extended to include: 260787004 |Physical object (physical object)|

    I can make this change but didn't know if I should since this is in a state of "Ready for Implementation"

    1. Yongsheng Gao

      Hi Penni Hernandez please make the changes since this template has not been picked up by the technical team.

  16. Penny Livesay

    Per the template, the FSN and PT both use "Inflammation of <body site>."  Many if not most existing concepts of this type use "<body structure>itis" as the FSN and PT, e.g. Appendicitis (disorder), Pancreatitis (disorder), Tonsillitis (disorder).  In fact, quite a few of these don't even have an "Inflammation of <body site>" synonym.  I believe this question has been raised previously, but I've looked at the Editorial Guide WIP and don't see new naming guidance.

    Should "<body structure>itis" be the PT, given its prevalent use?  One problem with this is that there are some body formula doesn't work for all body structures (e.g. inflammation of filtering bleb, inflammation of ampulla of Vater), but perhaps  "<body structure>itis" could be an optional description?