SNOMED CT Templates

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StatusIn PROD
Version

2.0

Descriptions:

Termdescription typeLanguage/acceptabilityLanguage/acceptabilityCase significance
[Course] Congenital [morphology] of [body structure] caused by [agent] (disorder)FSNus:Pgb:Pci
[Course] Congenital [morphology] of [body structure] caused by [agent]SYNus:Pgb:Pci


Concept model:

Attribute cardinalityAttributeValueRole group cardinality
1..1


116680003 |Is a (attribute)|


64572001 |Disease (disorder)|

N/A
0..1

263502005 |Clinical course (attribute)|

[Course] <   288524001 |Courses (qualifier value)|1..1
0..1

42752001 |Due to (attribute)|

<<  64572001 |Disease (disorder)|

1..1
1..1


246454002 |Occurrence (attribute)|


255399007 |Congenital (qualifier value)|

1..1
0..1


116676008 |Associated morphology (attribute)|


<< 49755003 |Morphologically abnormal structure (morphologic abnormality)|

0..1


363698007 |Finding site (attribute)|


<< 442083009 |Anatomical or acquired body structure (body structure)|

1..1

370135005 |Pathological process (attribute)|  

<<  308490002 |Pathological developmental process (qualifier value)|

0..1

[Agent]

<  105590001 |Substance (substance)|

OR

<  410607006 |Organism (organism)|

OR

< 78621006|Physical force (physical force)|


Definition status:  


900000000000073002 |Sufficiently defined concept definition status (core metadata concept)|

Applies to:

<  66091009 |Congenital disease (disorder)|

Template language:

64572001 |Disease (disorder)|   : [[~0..1]] {[[~0..1]]   263502005 |Clinical course (attribute)|   = [[ +id (<   288524001 |Courses (qualifier value)|   ) @course]]} , [[~0..1]] {[[~0..1]]   42752001 |Due to (attribute)|   = [[ +id (<<  64572001 |Disease (disorder)|   ) ]]} ,[[~1..1 @rolegroup]]{ [[~0..1]]   116676008 |Associated morphology (attribute)|  = [[+id(<<   49755003 |Morphologically abnormal structure (morphologic abnormality)|   ) @morphology ]], [[~0..1]]   363698007 |Finding site (attribute)|   = [[+id(<<  442083009 |Anatomical or acquired body structure (body structure)|  )]], [[~1..1]]  246454002 |Occurrence (attribute)|   =  255399007 |Congenital (qualifier value)| , [[~1..1]]   370135005 |Pathological process (attribute)|   = [[ +id (<<  308490002 |Pathological developmental process (qualifier value)| ) @proc]], [[~0..1]]  246075003 |Causative agent (attribute)|  = [[ +id (<  410607006 |Organism (organism)| OR <  105590001 |Substance (substance)|  OR  <  78621006 |Physical force (physical force)| ) @agent]] }

Link to the misaligned concept report:


Rules for description generation:

  1. Remove the semantic tag, e.g. (disorder)
  2. Remove 'congenital' from value of associated morphology.

JIRA ticket:

INFRA-5383 - Getting issue details... STATUS


14 Comments

  1. Jim Case

    Penni,

    This would only be a valid template for congenital conditions that result in morphological changes.  There are other types of congenital diseases that do not have morphologic changes (you probably realized that, but it is not clear on the template name).  In any case, we will also be extending the range of the PATHOLOGICAL PROCESS attribute in the near future so you also need

    PATHOLOGICAL PROCESS =  Pathological development process

  2. Yongsheng Gao

    Hi Jim Case, thanks for the feedback. The name is changed to include morphology and body structure for descriptions. We can update the template when the pathological process is ready for production. The batch change function in the iteration 3 development will update the concept modeling to the new template.

  3. Penni Hernandez

    Thanks Yong & Jim

  4. Jim Case

    Yongsheng Gao, can I get the template language added to this tracker?

    1. Yongsheng Gao

      Hi Jim Case, I added the template language. It looks like that we are having the same template for different subdomains of congenital disease, congenital malformation and congenital deformity. I am wondering if we should make |Pathological process| as optional for |Congenital disease|. 

      1. Jim Case

        Yongsheng Gao , lemme take a look.

        Currently Congenital deformity is a subtype of Congenital malformation. so should be covered by that template and there is no need for a separate congenital deformity template.  We might get away with having one template for the entire subhierarchy.  The direct subtypes of congenital disease that do not require a pathological process are typically metabolic diseases.  Let's go ahead and modify this as you suggest and see what falls out.  

  5. Yongsheng Gao

    The new format about the role group (indicated by colour) has been updated. This template is an update to the existing template in the authoring platform. It is renamed as version 2 and a new JIRA ticket has been raised for the implementation in the AP. 

  6. Jim Case

    Yongsheng Gao ,

    While we could debate the subject, I am wondering about whether we should add an optional DUE TO relationship when the congenital anomaly is a result of a disease in the mother.  For example, there is an increased risk of congenital heart defects in diabetic mothers, a number of congenital abnormalities associated with maternal toxoplasmosis, etc.

    1. Yongsheng Gao

      Hi Jim Case  The attribute 'due to' was excluded from templates in the past because it was not easy to determine if it is a 'complication' or not. As we discussed the new guidance on the association patterns, 'complication' is no longer required for a condition due to another condition.  Now, we can add optional 'due to' for this template. We might need to talk about the updates to other existing templates and possible optional attributes such as 'after' according to the new guidance.

      I also agree that this single template would be sufficient after the update and we do not need those two subtemplates.

      Suzanne Santamaria  could you please update this template and check content alignments?

      1. Suzanne Santamaria

        Yongsheng Gao , I updated the template and checked for content alignment. I'd like to discuss this further before I start working on the list as it is large (around 2000 concepts), e.g., is there a need to review the entire list now, or just focus on the content needed for the genomics project (limit to abnormal shape for analysis?)

        https://docs.google.com/spreadsheets/d/1lUQAYuMT7-gtCmlMzjHGC7Q-SuDYWgQ4ruOFJMLAn_s/edit#gid=0


        1. Yongsheng Gao

          Hi Suzanne Santamaria, I think it would be practical to address the abnormal shape for the genomics project if it is okay with you. The rest will need to be subdivided as part of the QI. As Jim Case noted, the pathological process can be optional for metabolic disease. We will need to find a way for the template to indicate when the pathological process is required or not. 

          1. Suzanne Santamaria

            Yongsheng Gao , I will start working on the congenital abnormal shape disorder concepts as part of QI:  QI-693 - Getting issue details... STATUS . 

  7. Jim Case

    Yongsheng Gao and Suzanne Santamaria ,

    In "all" cases of a congenital morphologic abnormality, there is a "Pathological development process", unless there is direct damage due to the causative agent.  My perception is that this would be a very limited number of concepts and so they would be exceptions to the template and do not need their own (less than 50 concepts). 

  8. Yongsheng Gao

    Following Jim's comments, I have approved the template for implementation.