SNOMED CT Templates

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StatusArchived
Version

0.8

Descriptions:

Termdescription typeLanguage/acceptabilityLanguage/acceptabilityCase significance

[course] infection caused by [bacteria] (disorder)

FSNus:Pgb:Pci[

[course] infection caused by [bacteria]

SYNus:Pgb:Pci


Concept model:

Attribute CardinalityAttributeValuerole group number
1..1

116680003 |Is a (attribute)|

64572001 |Disease (disorder)|

0
0..1

263502005 |Clinical course (attribute)|  


<  288524001 |Courses (qualifier value)|

0
1..1

370135005 |Pathological process (attribute)|

441862004 |Infectious process (qualifier value)|

1
0..1

116676008 |Associated morphology (attribute)|

409774005 |Inflammatory morphology (morphologic abnormality)| OR 23583003 |Inflammation (morphologic abnormality)|


1
1..1

246075003 |Causative agent (attribute)|

[Bacteria] << 409822003 |Superkingdom Bacteria (organism)|

1

Definition status:  


900000000000073002 |Defined (core metadata concept)|


Rules for description generation:

  1. Remove the semantic tag, e.g. (body structure)
  2. Remove 'Structure of' from [body structure] if term starts with 'Structure of'   e.g. 709530002|Structure of phalanx of hand (body structure)|
  3. Remove 'structure' from [body structure] if term contains 'structure', e.g. 69536005|Head structure (body structure)|   24097009|Bone structure of hand (body structure)|

JIRA ticket:

QI-56 - Getting issue details... STATUS

14 Comments

  1. Monica Harry

    Yongsheng Gao - do we consider this template complete and ready for implementation?

  2. Yongsheng Gao

    Monica Harry, I am not sure about the range for associated morphology. Should it always be << Inflammatory morphology? Should it allow morphology other than inflammation? The advice from Jim Case would help us to finalise the template. I think we could merge this template with the Infection of body structure caused by bacteria v2. 

  3. Monica Harry

    We could merge as you suggest but Finding site would then be optional. I am fine to broaden the range for Associated morphology.

  4. Jim Case

    Yong will get us a summary of the current usage of values for ASSOCIATED MORPHOLOGY

  5. Yongsheng Gao


    Jim Case, Please find the the summary of analysis for infectious diseases modelled with or without associated morphology.

    There are over 6,700 infectious diseases in the current release. Half of them (over 3,200) are modelled without associated morphology. The most common description patterns are:

    • disease caused by X,  or X disease
    • Infection caused by X,  X infection

    The rest of them are modelled by 240 different associated morphologies. They can be divided further by modeling with inflammatory morphology or not. 

    • 1,009 infectious diseases are modelled by 176 concepts that are not inflammatory morphology. 
    • 2,573 infectious diseases are modelled by 64 inflammatory morphology and its subconcepts. Among them,
      • 118 infectious diseases are modelled by exact 409774005|Inflammatory morphology|.
      • 1,240 infectious disease are modelled by exact 23583003|Inflammation (morphologic abnormality)| 

    1. Jim Case

      When you say 240 different morphologies, how many of these are not subtypes of Inflammation (scheduled to be inactivated) or Inflammatory morphology? Is it the 176 you mention?  Can you give me a listing?

  6. Yongsheng Gao

    Jim Case, yes, it is 176 morphologies that in the summary. Please find the attached tab delimited files for both infectious disease and morphologies are not inflammatory.

      

  7. Jim Case

    Yong,

    In looking at some of these morphologies, I am wondering if they are all in the same RG as the PATHOLOGICAL PROCESS?  Some of these don't look to be morphologies associated with infection, so it would be good to look at the association between the process and the structure.  Is there a way you can do that?

  8. Yongsheng Gao

    Hi Jim Case, among these 1009 infectious diseases, 825 of them are modelled by 'associated morphology' and 'pathologic process' in a single role group. The rest 184 are modelled without pathologic process in the same role group. Assoicated morphology and pathologic process in a single role group.tsv Associated morphology and pathologic process are not in a single role group.tsv

  9. Yongsheng Gao

    Jim Case, following our discussion at the meeting, I have created two templates.

    The first template is for 'infection' caused by bacteria with optional inflammatory morphology or inflammation.

    The second template is for specific morphologies other than inflammatory morphology or inflammation. These morphologies must be represented in the descriptions.

    Please let me know you thought. 

  10. Monica Harry

    Jim Case Yongsheng Gao - Thanks for this. Looks ready to me. Agree?

  11. Jim Case

    Yongsheng Gao, it looks like the "non-inflammatory" template does not have an optional "morphologic abnormality" relationship,  The other more complex template looks fine...

  12. Yongsheng Gao

    Jim Case I have updated the other template to include morphologic abnormality. We can still keep this simple template if it is simple for authoring, infection of X.  The other template has comprehensive coverage. 

    1. Jim Case

      Optional body structure?