Descriptions:
Term | description type | Language/acceptability | Language/acceptability | Case Significance |
---|---|---|---|---|
[Accidental/Intentional] Poisoning caused by [agent] due to [event] (disorder) | FSN | us:P | gb:P | ci |
[Accidental/Intentional] Poisoning caused by [agent] due to [event] | SYN | us:P | gb:P | ci |
[Accidental/Intentional] [Agent] poisoning due to [event] | SYN | us:A | gb:A | ci |
Concept model:
Attribute cardinality | Attribute cardinality in role group | Attribute | Value |
---|---|---|---|
1..1 | 0..0 | ||
0..1 | 0..1 | ||
0..1 | 0..1 | ||
0..2 | 1..1 | ||
0..1 | |||
0..1 | |||
0..1 |
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
[[~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)| ) ]]}
- 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:
- Apply General rules for generating descriptions for templates
- Remove the word 'event' and semantic tag from the value of |Due to|
Jira tickets
- INFRA-12455Getting issue details... STATUS
EDITORIAL GUIDELINES for Causative agent (attribute):
Hierarchy | Concept type | Allowed | Exception | Examples and Notes |
---|---|---|---|---|
Substance | Base | yes | none | Poisoning concepts representing a substance base should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|. Examples:
Classification results are expected to be consistent with the modeling of the concept selected as the Causative agent in the Substance hierarchy. |
Substance | Modification | no | yes | 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:
Examples:
|
Substance | Structure grouper | yes | none | Poisoning concepts representing a structure grouper should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|. Examples:
Classification results are expected to be consistent with the modeling of the concept selected as the Causative agent in the Substance hierarchy. |
Substance | Disposition grouper | yes | none | Poisoning concepts representing a disposition grouper should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|. Examples:
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. |
Substance | Role grouper | no | none | Poisoning concepts representing a Role grouper should be modeled using a Causative agent that is a descendant of 105590001 |Substance (substance)|. Example:
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. |
Product | Structure grouper | no | none | 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. |
Product | Disposition grouper | no | none | 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. |
Product | Role grouper | yes | none | Examples to be added - pending implementation of roles and products as causative agents |
Product | Medicinal product-containing | yes | none | Examples to be added - pending implementation of roles and products as causative agents |
Product | Medicinal product-only | no | none | 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. |
Product | Medicinal product form-containing | no | none | No 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. |
Product | Medicinal product form-only | no | none | No 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. |
Product | Clinical drug | no | none | No 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
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
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
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
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?
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?
Thanks,
Farzaneh
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.
Yongsheng Gao
I second that.
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
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.
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.
Farzaneh Ashrafi
Thanks Yongsheng Gao. This is great to know.
Farzaneh Ashrafi
Updated the template by adding other optional attributes as result of the following discussion: GC-911 - Getting issue details... STATUS
Farzaneh Ashrafi
Hi Yongsheng Gao,
This template is ready for implementation. Can you kindly review and raise the ticket?
Thanks,
Farzaneh
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
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
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:
I have also updated the "Applies to", "Template Language", and "Link to the misaligned concept report" sections of the template.
Thanks,
Farzaneh
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?
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
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:
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).
(<< 75478009 |Poisoning (disorder)| ) MINUS (<< 1149322001 |Intoxication (disorder)| OR << 1149222004 |Overdose (disorder)| )
Please let me know if you have any questions.
Thanks,
Farzaneh