SNOMED CT Templates

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StatusReady for implementation
Version1.0

Descriptions:

Termdescription typeLanguage/acceptabilityLanguage/acceptabilityCase Significance
[Accidental/Intentional] Poisoning caused by [agent] due to [event] (disorder)FSNus:Pgb:Pci
[Accidental/Intentional] Poisoning caused by [agent] due to [event] 
SYNus:Pgb:Pci
[Accidental/Intentional] [Agent] poisoning due to [event]SYNus:Agb:Aci

Concept model:

Attribute cardinalityAttribute cardinality in role groupAttributeValue
1..10..0

116680003 |Is a (attribute)|

75478009 |Poisoning (disorder)|

0..10..1

263502005 |Clinical course (attribute)|

<  288524001 |Courses (qualifier value)|

0..10..1

42752001 |Due to (attribute)|

<  272379006 |Event (event)|

0..21..1

246075003 |Causative agent (attribute)|

[agent] <<  105590001 |Substance (substance)|  OR <<  373873005 |Pharmaceutical / biologic product (product)|  OR <<  410607006 |Organism (organism)|

0..1

363698007 |Finding site (attribute)|

<  123037004 |Body structure (body structure)|

0..1

370135005 |Pathological process (attribute)|

<  308489006 |Pathological process (qualifier value)|

0..1

116676008 |Associated morphology (attribute)|

<  49755003 |Morphologically abnormal structure (morphologic abnormality)|

Definition status:  


900000000000073002 |Defined (core metadata concept)|

Applies to

Poisoning caused by substance, product, or organism excluding "Overdose", and "Intoxication" (which have their own templates):


(<<  75478009 |Poisoning (disorder)| ) MINUS (<<  1149322001 |Intoxication (disorder)|  OR <<  1149222004 |Overdose (disorder)|  )

Template Language

75478009 |Poisoning (disorder)| : 
[[~0..1]] {[[~0..1]]  263502005 |Clinical course (attribute)|  = [[ +id ( <  288524001 |Courses (qualifier value)|  ) @course]]}, 
[[~0..1]] {[[~0..1]]  42752001 |Due to (attribute)|  = [[ +id ( <  272379006 |Event (event)|  ) @dueto ]]}, 
[[~0..2 @rolegroup]] { 
[[~1..1]]  246075003 |Causative agent (attribute)|  = [[+id (( <<  105590001 |Substance (substance)|  OR <<  373873005 |Pharmaceutical / biologic product (product)| ) OR <<  410607006 |Organism (organism)|  ) @causative]], 
[[~0..1]]  363698007 |Finding site (attribute)|  = [[+id ( <<  123037004 |Body structure (body structure)|  ) ]], 
[[~0..1]]  370135005 |Pathological process (attribute)|  = [[+id ( <<   308489006 |Pathological process (qualifier value)|  ) ]], 
[[~0..1]]  116676008 |Associated morphology (attribute)|  = [[+id ( <<  49755003 |Morphologically abnormal structure (morphologic abnormality)|  ) ]]}
Note:

  • Pathological process is added to include content under food poisoning.
  • Addition of other attributes such as "246454002 |Occurrence (attribute)|, 363714003 |Interprets (attribute)|, and 363713009 |Has interpretation (attribute)| was considered. However, they were not added due to the very low number of concepts defined by them. Same consideration was applied to expanding the range for 42752001 |Due to (attribute)| to include 71388002 |Procedure (procedure)|, 
     and/or 64572001 |Disease (disorder)| i.e. they were not added as valid values for due to attribute because only a very small number of concepts are defined by them.

Link to the misaligned concept report

https://docs.google.com/spreadsheets/u/0/d/1G-cOv78CFHDprzBYWvb8b2WRCu-PsNxp-0vlzG716nQ/edit

Rules for generating descriptions:

  1. Apply General rules for generating descriptions for templates
  2. Remove the word 'event' and semantic tag from the value of |Due to|

Jira tickets

INFRA-12455 - Getting issue details... STATUS

EDITORIAL GUIDELINES for Causative agent (attribute):

Hierarchy

Concept type

Allowed

Exception

Examples and Notes

SubstanceBaseyesnone

Poisoning concepts representing a substance base should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|.

Examples:

  • 13503000 |Poisoning caused by naloxone (disorder)|
  • 30138004 |Poisoning caused by ether (disorder)|

Classification results are expected to be consistent with the modeling of the concept selected as the Causative agent in the Substance hierarchy.

SubstanceModificationnoyes

Poisoning concepts representing a substance modification should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|. Concepts representing substance modifications are exceptions and may be included if the poisoning profile is significantly different from the substance base.

Exception examples:

  • Salt forms (e.g. 273948005 |Chloral hydrate (substance)|, 396063006 |Fluphenazine decanoate (substance)|)

Examples:

  • 62942003 |Tetraethyl pyrophosphate poisoning (disorder)|
SubstanceStructure grouperyesnone

Poisoning concepts representing a structure grouper should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|.

Examples:

  • 1153528004 |Poisoning caused by substance with ether structure (disorder)|

Classification results are expected to be consistent with the modeling of the concept selected as the Causative agent in the Substance hierarchy.

SubstanceDisposition grouperyesnone

Poisoning concepts representing a disposition grouper should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|.

Examples:

  • 9291000 |Poisoning caused by monoamine oxidase inhibitor (disorder)|

Classification results are expected to reflect that the adverse reaction concepts are descendants of the appropriate disposition grouper based on the modeling of the 726542003 |Has disposition (attribute)| attribute in the substance hierarchy.

SubstanceRole groupernonone

Poisoning concepts representing a Role grouper should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|.

Example:

  • 241748001 |Poisoning caused by analgesic drug (disorder)|

Classification results are expected to reflect that the adverse reaction concepts are descendants of the appropriate disposition grouper based on the modeling of the 726542003 |Has disposition (attribute)| attribute in the substance hierarchy.

ProductStructure groupernonone

No use case has been identified for use of this concept type for modeling in this subhierarchy. Medicinal product-containing concepts can be used for modeling in this subhierarchy.


ProductDisposition groupernononeNo use case has been identified for use of this concept type for modeling in this subhierarchy. Medicinal product-containing concepts can be used for modeling in this subhierarchy.
ProductRole grouperyesnone

Examples to be added - pending implementation of roles and products as causative agents

ProductMedicinal product-containingyesnone

Examples to be added - pending implementation of roles and products as causative agents

ProductMedicinal product-onlynononeNo use case has been identified for use of this concept type for modeling in this subhierarchy. Medicinal product-containing concepts can be used for modeling in this subhierarchy.
ProductMedicinal product form-containingnononeNo use case has been identified for use of this concept type for modeling in this subhierarchy. Medicinal product form-containing concepts can be used for modeling in this subhierarchy.
ProductMedicinal product form-onlynononeNo use case has been identified for use of this concept type for modeling in this subhierarchy. Medicinal product form-containing concepts can be used for modeling in this subhierarchy.
ProductClinical drugnononeNo use case has been identified for use of this concept type for modeling in this subhierarchy. Medicinal product form-containing concepts can be used for modeling in this subhierarchy.

19 Comments

  1. Farzaneh Ashrafi

    Hi Peter G. Williams

    As discussed in today's call, I cannot get the template language posted above to work in the reporting platform (QI -Template Compliance). Can you please take a look and let me know what the problem might be?

    Thanks,

    Farzaneh

    CC: Yongsheng Gao

    1. Peter G. Williams

      Hi Farzaneh Ashrafiyes the reason I wasn't seeing any problems with the template language there is because the error was actually being thrown in some utility routine that had nothing to do with the parser, so I think the STL is probably fine.    There must be something in that data set that's causing it to be thrown out.   I'll investigate further...

      Yes, something about trying to populate FSNs in the logical template and failing to populate an SCTID.   I'll raise an RP ticket for it....INFRA-6388

  2. Farzaneh Ashrafi

    Hi Jim Case and Yongsheng Gao

    Can you kindly review the template and let me know if you have any feedback? The template is created based on the EAG recommendation on poisoning and overdose during the following meetings:

    Thanks,

    Farzaneh

    CC: Toni Morrison

  3. Jim Case

    Farzaneh Ashrafi,

    This is a pretty generic template without many constraints on the value for DUE TO.  Are we using that for more than accidental or intentional?


    1. Farzaneh Ashrafi

      Hi Jim Case,

      I don't think any other values rather than accidental and intentional events would be used here. Perhaps I should change the value for "due to" to the following to make it more accurate?

      • <<  1148742001 |Intentional event (event)| OR <<  418019003 |Accidental event (event)|

      Thanks,

      Farzaneh

  4. Jim Case

    If we think that there are no other values that would be acceptable, then that would prevent people from using other types of events to define the poisonings.

    1. Yongsheng Gao

      I second that.

      1. Farzaneh Ashrafi

        Thank you All. I changed the attribute value range as requested--and as discussed in the internal call today with Jim while reviewing the list of "Due to" attributes for 7895008 |Poisoning caused by drug AND/OR medicinal substance (disorder)| and 441952005 |Poisoning caused by chemical substance (disorder), as well as 75478009 |Poisoning (disorder)|.

        We also discussed that the focus of this template is poisoning by "substance or medicinal product" and agreed that separate templates are required for "Food poisoning" and "poisoning due contact with organism". They will be created as this project progresses.

        Thanks, 

        Farzaneh

  5. Toni Morrison

    Just FYI - For the new Device attributes, Yong has indicated that adding an additional value at a later date is not a long arduous process so we are moving that direction with several device attributes.

  6. Yongsheng Gao

    Hi Farzaneh Ashrafi, I have updated the format for concept model and template language. The change is that these three attributes are self-grouped. They should not be grouped in a single role group.  

  7. Farzaneh Ashrafi

    Thanks Yongsheng Gao. This is great to know.

  8. Farzaneh Ashrafi

    Updated the template by adding other optional attributes as result of the following discussion:  GC-911 - Getting issue details... STATUS

  9. Farzaneh Ashrafi

    Hi Yongsheng Gao,

    This template is ready for implementation. Can you kindly review and raise the ticket?

    Thanks,

    Farzaneh

  10. Farzaneh Ashrafi

    Hi Yongsheng Gao

    I confirmed with Jim Case today that it is okay to add an additional value to the "Due To" attribute for poisoning due to exposure to/contact with an organism or physical object (which is consistent with what we did for contact dermatitis). I have updated the template including the version number accordingly.

    Thanks,

    Farzaneh

  11. Yongsheng Gao

    Hi Farzaneh Ashrafi, I have changed the cardinality from 0..1 to 1..1 for the causative agent as it should be mandated. The range restrictions in the template language are also updated to align with the model.  Please let me know if you are okay with the changes. 

    Cheers,

    Yong

  12. Farzaneh Ashrafi

    Hi Yongsheng Gao 

    Following the discussion on September 14  during the QI call, I have updated this template to expand its use for concepts of type poisoning by organism. The following changes have been applied to the concept model:

    • Add organism as acceptable value for causative agent
    • Expand range of due to: <272379006 |Event (event)|

    I have also updated the "Applies to", "Template Language", and "Link to the misaligned concept report" sections of the template. 

    Thanks,

    Farzaneh

  13. Yongsheng Gao

    Hi Farzaneh Ashrafi , I just noticed that  441952005 |Poisoning caused by chemical substance (disorder)| has been inactivated. The concept has been used in the ECL for defining the scope of this template. We need to check if anything else needs to be updated. There are about 130 misaligned concepts (44 concepts in your report) after replacing this concept with Poisoning. https://docs.google.com/spreadsheets/d/1sIrJWwZfRqgzVPUon9Ek45ud9OuJvT543kQxGSHIfdE/edit#gid=0. Could you please check if any further updates are needed to this template?

    1. Farzaneh Ashrafi

      Hi Yongsheng Gao 

      Thanks for letting me know. I will review the misaligned report and will let you know of required changes. Can you let me know what is the priority on this?

      Thanks again,

      Farzaneh

  14. Farzaneh Ashrafi

    Hi Yongsheng Gao 

    As discussed I have updated the template for poisoning (Kept version as 1.0 as it is not yet implemented).

    Here is a summary of changes we agreed on:

    • Changed the cardinality for role grouper containing causative agent to 0..2 so that the template can be applied to:
      • High level groupers such as Accidental poisoning, Food poisoning, etc. where no value for causative agent can be assigned.
      • Concepts that contain more than one causative agent (mainly concepts that contain one causative agent as organism and one as substance).
      • Concepts defined by non-medicinal products that cannot be created just yet e.g. "Accidental poisoning by oil colors (disorder)"
    • Added Pathological process as an acceptable attribute so that the template can be applied for subtypes of Food poisoning (note added above)
    • Updated template language to account for changes noted above.
    • Addition of other attributes such as "246454002 |Occurrence (attribute)|, 363714003 |Interprets (attribute)|, and 363713009 |Has interpretation (attribute)| was considered. However, they were not added due to the very low number of concepts defined by them. Same consideration was applied to expanding the range for 42752001 |Due to (attribute)| to include 71388002 |Procedure (procedure)|, 
       and 64572001 |Disease (disorder)| i.e. they are not added as valid values due to very small number of concepts defined by them (Note added above).
    • Changed "Applies to" to a more general and streamlined query: 
      (<<  75478009 |Poisoning (disorder)| ) MINUS (<<  1149322001 |Intoxication (disorder)|  OR <<  1149222004 |Overdose (disorder)|  )
    • Updated the template misaligned report (now containing 28 terms, all considered acceptable exceptions).
    • Changed status to ready for review.

    Please let me know if you have any questions.

    Thanks,

    Farzaneh