SNOMED CT Templates

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StatusReady for implementation
Version

1.0

Descriptions:

Termdescription typeLanguage/acceptabilityLanguage/acceptabilityCase significance
[Access] [biopsy device] biopsy of [morphology] of [body structure] using [imaging] guidance (procedure)FSNus:Pgb:Pci
[Imaging] guided [access] [biopsy device] biopsy of [morphology] of [body structure]PTus:Pgb:Pci
[Access] [biopsy device] biopsy of [morphology] of [body structure] using [imaging] guidanceSYNus:Agb:Aci

Example: 16446481000119106 |Percutaneous core needle biopsy of thyroid using ultrasonographic guidance (procedure)|


Concept model: 

Attribute Group CardinalityAttribute Cardinality

Attribute in Group Cardinality

AttributeValue
0..01..1

116680003 |Is a (attribute)|

71388002 |Procedure (procedure)|

1..2
0..1

260507000 |Access (attribute)|

<  309795001 |Surgical access values (qualifier value)|


1..1

260686004 |Method (attribute)|


[imaging] <<  360037004 |Imaging - action (qualifier value)|  


0..1

405813007 |Procedure site - Direct (attribute)|

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


1..1

363703001 |Has intent (attribute)|

429892002 |Guidance intent (qualifier value)|


0..1

424361007 |Using substance (attribute)|

385420005 |Contrast media (substance)|


0..1

424226004 |Using device (attribute)|

<< 262182009 |Stereotactic device (physical object)|


0..1

425391005 |Using access device (attribute)|


<< 49062001 |Device (physical object)|

1..2
0..1

260507000 |Access (attribute)|

[Access] <  309795001 |Surgical access values (qualifier value)|


1..1

260686004 |Method (attribute)|


<<  129314006 |Biopsy - action (qualifier value)|


0..1

405813007 |Procedure site - Direct (attribute)|

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


0..1

363700003 |Direct morphology (attribute)|

[morphology] <<   49755003 |Morphologically abnormal structure (morphologic abnormality)|  


0..1

424226004 |Using device (attribute)|

[biopsy device] <<  118377000 |Biopsy needle, device (physical object)|  OR << 22566001 |Cytology brush, device (physical object)|  OR << 360237009 |Vacuum aspirator (physical object)|


0..1

425391005 |Using access device (attribute)|

<< 49062001 |Device (physical object)|

Definition status:  


900000000000073002 |Sufficiently defined by necessary conditions definition status (core metadata concept)|

Applies To:

<<  71388002 | Procedure (procedure)|  :  260686004 | Method (attribute)|  = <<  129314006 | Biopsy - action (qualifier value)|  and  260686004 | Method (attribute)|  = <<  360037004 | Imaging - action (qualifier value)|

Template language: 

71388002 |Procedure (procedure)|  : 
[[~1..2]] { 
[[~0..1]]  260507000 |Access (attribute)|  = [[+id ( <  309795001 |Surgical access values (qualifier value)|  ) @Accessaction1]],[[~1..1]]  260686004 |Method (attribute)|  = [[ +id ( <<  360037004 |Imaging - action (qualifier value)| ) @Imagingaction ]], 
[[~0..1]]  405813007 |Procedure site - Direct (attribute)|  = [[ +id (<  442083009 |Anatomical or acquired body structure (body structure)| ) @Bodystructure1 ]],
[[~1..1]]  363703001 |Has intent (attribute)|  =  429892002 |Guidance intent (qualifier value)| ,[[~0..1]]  424361007 |Using substance (attribute)|  =  385420005 |Contrast media (substance)| , [[~0..1]]  424226004 |Using device (attribute)|  = [[ +id ( << 262182009 |Stereotactic device (physical object)| ) @Usingdevice ]],[[~0..1]]  425391005 |Using access device (attribute)|  = [[ +id ( << 49062001 |Device (physical object)| ) @Usingaccessdevice1 ]] },
[[~1..2]] { 
[[~0..1]]  260507000 |Access (attribute)|  = [[+id ( <  309795001 |Surgical access values (qualifier value)|  ) @Accessaction2]],
[[~1..1]]  260686004 |Method (attribute)|  = [[+id ( <<  129314006 |Biopsy - action (qualifier value)|  ) @Biopsyaction]],
[[~0..1]]  405813007 |Procedure site - Direct (attribute)|  = [[+id (<  442083009 |Anatomical or acquired body structure| ) @Bodystructure2 ]],
[[~0..1]]  363700003 |Direct morphology (attribute)|  = [[+id(<<  49755003 |Morphologically abnormal structure (morphologic abnormality)|  ) @Morphology]], 
[[~0..1]]  424226004 |Using device (attribute)|  = [[+id(<<  118377000 |Biopsy needle, device (physical object)|  OR << 22566001 |Cytology brush, device (physical object)|  OR << 360237009 |Vacuum aspirator (physical object)| ) @Biopsydevice]],[[~0..1]]  425391005 |Using access device (attribute)|  = [[ +id ( << 49062001 |Device (physical object)| ) @Usingaccessdevice2 ]] }

Link to the misaligned concept report:

https://docs.google.com/spreadsheets/d/1e13y7cb48bgKjjZKK-s-bJrKwty6zmCir9fA0P5oLx0/edit?usp=sharing

Rules for description generation: 

  1. Apply General rules for generating descriptions for templates;
  2. Apply Enhancements for the Template Language;
  3. For magnetic resonance imaging guidance, the naming should be FSN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using magnetic resonance imaging guidance (procedure), PT: MRI guided [access] [biopsy needle] biopsy of [morphology] of [body structure] - This PT should use case significance CS, SYN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using magnetic resonance imaging guidance.
  4. For computed tomography guidance, the naming should be FSN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using computed tomography guidance (procedure), PT: CT guided [access] [biopsy needle] biopsy of [morphology] of [body structure] - This PT should use case significance CS, SYN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using computed tomography guidance.
  5. For ultrasonography guidance, the naming should be FSN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using ultrasonographic guidance (procedure), PT: Ultrasonography guided [access] [biopsy needle] biopsy of [morphology] of [body structure], SYN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using ultrasonographic guidance, SYN: [Access] [biopsy needle] biopsy of [morphology] of [body structure] using ultrasound guidance.
  6. For percutaneous fine needle aspiration biopsy, the descriptions should follow this example format: FSN: Percutaneous fine needle aspiration biopsy of X (procedure), PT: Percutaneous fine needle aspiration biopsy of X, SYN: Percutaneous fine needle aspiration of X, SYN: Percutaneous fine needle biopsy of X. Imaging guidance should be inserted in descriptions as appropriate.

JIRA ticket:

QI-940 - Getting issue details... STATUS QI-941 - Getting issue details... STATUS

INFRA-8933 - Getting issue details... STATUS


15 Comments

  1. Sarah Warren

    Hi Yongsheng Gao, would you be able to review this template? I have run the misaligned report and the main correction needed is that the USING DEVICE should be <<  118377000 |Biopsy needle, device (physical object)|. This has also been raised in a Freshdesk ticket: https://ihtsdo.freshdesk.com/a/tickets/36588

    cc. Monica Harry  

    1. Yongsheng Gao

      Hi Sarah Warren, the restricted domain of 'needle biopsy' is useful to address the issue raised by the fresh-desk ticket. So, you can update the biopsy needle to fix the issues. I have extended the domain to make it a generic template for imaging guided biopsy procedures. Since the using device has been restricted to biopsy needle, the new content of this template will not have the current issue anymore. 

      However, this has raised a weakness in the current template compliance query. When an attribute is optional, e.g. using device, the template query does not seem to check if the value is within the range when the attribute is present in a concept model. For example, the optional attribute 'using device' in the template has the range constraint of biopsy needle. If a imaging guided biopsy concept is modelled by using 'needle device', the template compliance should report an error because the value is not within the specified range of this attribute.  Peter G. Williams could you please check if this is considered in the current script for the template compliance report? 

      1. Peter G. Williams

        Hi, yes absolutely the attribute value should fall within the range specified by the slot, regardless of the cardinality on the attribute.    If you see any example of this failing to report as an error please do let me know and I'll investigate.

        Checking this just now in Dev, I see no concepts failing to align to the template.   I'll change one to Using Device → Needle device and check it gets picked up.

        Here's the before: https://docs.google.com/spreadsheets/d/1QSzYItpgvkQfTFCI8_visRdsWlyIpUQK46xH41A2IuA/edit#gid=5

        And the after: https://docs.google.com/spreadsheets/d/10lO8gZCliSAF6k4JdiHNHVTzNw78nN6A-Il5BGlJK6w/edit#gid=0

        Yes that concept that I changed from fine needle to needle device is now picked up as failing compliance.   It makes me happy when code behaves as it's expected to.

        I don't know if it's in the scope of your question, but the MRCM is not considered in template compliance since templates are expected to be more restrictive than MRCM rules.   In the future it would be good to validate the templates themselves as they're created, to ensure they are consistent with the MRCM.

        1. Yongsheng Gao

          Hi Peter G. Williams, thanks for doing the testing. The example template query can be found in this link https://docs.google.com/spreadsheets/d/1EpveeQLGoCFEwKwpPaYulR8QQtwGjQVgowLcFGfPWzA/edit#gid=1

          It does not report any issues though some imaging guided needle biopsy procedures are still modelled by 'needle, device' in current production main, for example, 

          16559741000119107 |Percutaneous needle biopsy of cyst of spinal cord using computed tomography guidance (procedure)|, 

          16520921000119109 |Percutaneous needle biopsy of muscle using fluoroscopic guidance (procedure)|, 

          408041000119104 |Percutaneous needle biopsy of pleura using computed tomography guidance (procedure)|

          1. Peter G. Williams

            Well well well.   There's something odd going on here, because those concepts are not showing up on any tab.   They should be one of either :   Misaligned, Aligned or Excluded.

            Leave it with me and I'll raise a ticket assuming there's a code fix required.

            1. Peter G. Williams

              Ah, found it.  In the last release I had a request to normalise concepts based on the stated hierarchy and I put in a switch so I could work with either, but I double clicked instead of single clicking and long story short there's now a code fault in Prod where all ECL recovered from the TS is being done in the stated view.   So that's why we're not picking up as many concepts as we'd expect.    I'll run the query locally to prove I've fixed this, but we'll need to have a discussion with Sonja Ulrich about when we can get a fix to Prod.   Actually it won't always happen as simple ECL is normally run in Memory, but for Template Compliance, we recover it from TS before memory has been populated.


              1. Peter G. Williams

                With the fix to ensure we're using in inferred hierarchy in place in Dev (and Prod data was copied in there yesterday ), we now pick up these Needle device infractions you were expecting to see:

                https://docs.google.com/spreadsheets/d/1-q_N0EQvulLIIczRRwjNGrWRBbneWzqPHI-wm_AUMuE/edit#gid=0

                Yongsheng Gao Sarah Warren

                1. Sarah Warren

                  Thanks Peter G. Williams

                2. Yongsheng Gao

                  Thanks Peter G. Williams, please fix the bug in the PROD report platform. So we can get correct results for template conformance report. 

  2. Sarah Warren

    Hi Yongsheng Gao I have now corrected the concepts in the misaligned report and Peter has rerun the report: https://docs.google.com/spreadsheets/d/1XSRlicNzQ4HLWkN3wOjPcQGScKLL-Y-Cr2ULGjot0Go/edit?usp=sharing While correcting the misaligned concepts I tweaked the template and template language so it would not pick up concepts that were actually correct. 7 concepts remain on the misaligned report: 77337009 |Stereotactic biopsy by aspiration of intracranial lesion (procedure)| has been corrected, the rest look correct and could be removed from the misaligned report by adding optional 425391005 |Using access device (attribute)| relationship to each relationship group in the template, but I wasn't sure how much this was needed for 4-5 concepts.


    1. Yongsheng Gao

      Hi Sarah Warren, let's include |Using access device| as optional in both role groups, the template will support the endoscopic ultrasonography guided biopsy procedures. So, we do not have any exceptions for this template.

      If the following ECL is the domain, you will find over 30 imaging and biopsy procedures. Should they be revised to imaging guided biopsy procedures? I think they are out of scope of this template. They could be addressed by a new general template for imaging guided biopsy. 

      << 71388002 |Procedure (procedure)| :
      260686004 |Method (attribute)| = << 129314006 |Biopsy - action (qualifier value)|
      and 260686004 |Method (attribute)| = << 360037004 |Imaging - action (qualifier value)|

      https://docs.google.com/spreadsheets/d/1DHg9JWXzyXE-iQCLRjW4w4HOkAvRu_aL8MgjrU9NiU0/edit#gid=0.



  3. Sarah Warren

    Hi Yongsheng GaoI have now updated the template and template language, adding |Using access device|. From looking at the report from the ECL you suggested, I think I need to review each of these 30+ concepts, perhaps raising a GC ticket to find out whether e.g. Ultrasound scan and biopsy of liver (procedure) is considered the same as Biopsy of liver using ultrasound guidance (procedure)? I'm not sure how much a new template would differ from this one - is it possible to use this template and change the 'Applies to' to the ECL query you suggested?

    1. Yongsheng Gao

      Hi Sarah Warren it sounds like a good plan. We can generalise this template for imaging guided biopsy.

  4. Sarah Warren

    Hi Yongsheng Gao I have now corrected the concepts in the rerun misaligned report. 3 concepts remain, though 1 is to be followed up on and may be changed to conform to this template. What are the next steps I need to do for this template? BW, Sarah

    https://docs.google.com/spreadsheets/d/1e13y7cb48bgKjjZKK-s-bJrKwty6zmCir9fA0P5oLx0/edit?usp=sharing

    1. Yongsheng Gao

      Thanks Sarah Warren I have raised a ticket for technical implementation.