Re: SNOMED CT constraint syntax - for querying instances or terminology?

[Bert Verhees]

I am following this discussion with great interest, just wanted you and 
Michael to know, just in case you would want to stop it or have it 
private, which I would regret.


Bert

On 30-09-15 09:20, Thomas Beale wrote:
ok - so the query would be applied to instances in a drug database 
(each instance there is a drug descriptor)?



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Re: SNOMED CT constraint syntax - for querying instances or terminology?

[Michael.Lawley]

This is indeed the intent: the language has been design to cater exactly for 
this extension.  I can't say that there's any international content about to 
come out with this addition numeric modelling, but Australia has been 
publishing this kind of content in the Australian Medicines Terminology (AMT) 
since July 2014 (one release per month).

Michael

Sent from my iPhone

On 1 Oct 2015, at 6:43 PM, David Moner 
> wrote:

Hello,

At this point I think that is the only option. I want to believe that the 
SNOMED CT Expression Constraint Language has been designed with a future 
evolution of SNOMED CT in mind, where concepts will be enriched with numerical 
values. For example, SNOMED CT now contains a set of Virtual Medical Products 
(VMP) such as "[374649006] Amoxicillin 400mg/5mL suspension (product)" with two 
relationships:
- Has active ingredient →  Amoxicillin
- Has dose form →  Oral suspension
If these relationships are enriched with the medication strength, then the VMP 
concepts would be better defined and could be queried using the numerical 
options of the constraint language.


2015-09-30 9:20 GMT+02:00 Thomas Beale 
>:
On 30/09/2015 07:51, michael.law...@csiro.au 
wrote:
Imagine instead the example was using the corresponding AMT concepts (since 
snomed pure doesn't have any concrete domain modelling -- I.e. numeric values).

Then the focus concept would be the AMT amoxycillin Medicinal Product concept 
2141501136100 and the constraint matches would be MPUUs and TPUUs with 
capsule form and between 500 and 800 mg of amoxycillin as an active ingredient


ok - so the query would be applied to instances in a drug database (each 
instance there is a drug descriptor)?

- thomas

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--
David Moner Cano
Grupo de Informática Biomédica - IBIME
Instituto ITACA
http://www.ibime.upv.es
http://www.linkedin.com/in/davidmoner

Universidad Politécnica de Valencia (UPV)
Camino de Vera, s/n, Edificio G-8, Acceso B, 3ª planta
Valencia – 46022 (España)
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Re: SNOMED CT constraint syntax - for querying instances or terminology?

[David Moner]

Hello,

At this point I think that is the only option. I want to believe that the
SNOMED CT Expression Constraint Language has been designed with a future
evolution of SNOMED CT in mind, where concepts will be enriched with
numerical values. For example, SNOMED CT now contains a set of Virtual
Medical Products (VMP) such as "[374649006] Amoxicillin 400mg/5mL
suspension (product)" with two relationships:
- Has active ingredient →  Amoxicillin
- Has dose form →  Oral suspension
If these relationships are enriched with the medication strength, then the
VMP concepts would be better defined and could be queried using the
numerical options of the constraint language.


2015-09-30 9:20 GMT+02:00 Thomas Beale :

> On 30/09/2015 07:51, michael.law...@csiro.au wrote:
>
> Imagine instead the example was using the corresponding AMT concepts
> (since snomed pure doesn't have any concrete domain modelling -- I.e.
> numeric values).
>
> Then the focus concept would be the AMT amoxycillin Medicinal Product
> concept 2141501136100 and the constraint matches would be MPUUs and
> TPUUs with capsule form and between 500 and 800 mg of amoxycillin as an
> active ingredient
>
>
> ok - so the query would be applied to instances in a drug database (each
> instance there is a drug descriptor)?
>
> - thomas
>
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>



-- 
David Moner Cano
Grupo de Informática Biomédica - IBIME
Instituto ITACA
http://www.ibime.upv.es
http://www.linkedin.com/in/davidmoner

Universidad Politécnica de Valencia (UPV)
Camino de Vera, s/n, Edificio G-8, Acceso B, 3ª planta
Valencia – 46022 (España)
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Re: SNOMED CT constraint syntax - for querying instances or terminology?

[Thomas Beale]

Hi Michael,

in that case, to what information base or DB could the amoxycillin query 
be applied? What is it for?


thanks

- thomas

On 29/09/2015 23:19, michael.law...@csiro.au wrote:

Hi Thomas,

These constraints are essentially queries over the snomed definitional 
content (ie the Relationships), not queries over external data (ie not 
EHRs).  The intent is to identify sets of snomed concepts that satisfy 
the constraint criteria. These sets could be subsequently used to join 
against/filter records in an EHR/EMR.


Work is ongoing for a full featured query language to address this 
larger problem, but the expression constraint language can be used to 
great effect when combined with SQL or other database tech to query 
health records.




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Re: SNOMED CT constraint syntax - for querying instances or terminology?

[Michael.Lawley]

Imagine instead the example was using the corresponding AMT concepts (since 
snomed pure doesn't have any concrete domain modelling -- I.e. numeric values).

Then the focus concept would be the AMT amoxycillin Medicinal Product concept 
2141501136100 and the constraint matches would be MPUUs and TPUUs with 
capsule form and between 500 and 800 mg of amoxycillin as an active ingredient

Michael

Sent from my iPhone

On 30 Sep 2015, at 4:34 PM, Thomas Beale 
> 
wrote:


Hi Michael,

in that case, to what information base or DB could the amoxycillin query be 
applied? What is it for?

thanks

- thomas

On 29/09/2015 23:19, michael.law...@csiro.au 
wrote:
Hi Thomas,

These constraints are essentially queries over the snomed definitional content 
(ie the Relationships), not queries over external data (ie not EHRs).  The 
intent is to identify sets of snomed concepts that satisfy the constraint 
criteria. These sets could be subsequently used to join against/filter records 
in an EHR/EMR.

Work is ongoing for a full featured query language to address this larger 
problem, but the expression constraint language can be used to great effect 
when combined with SQL or other database tech to query health records.


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Re: SNOMED CT constraint syntax - for querying instances or terminology?

[Thomas Beale]

On 30/09/2015 07:51, michael.law...@csiro.au wrote:
Imagine instead the example was using the corresponding AMT concepts 
(since snomed pure doesn't have any concrete domain modelling -- I.e. 
numeric values).


Then the focus concept would be the AMT amoxycillin Medicinal Product 
concept 2141501136100 and the constraint matches would be MPUUs 
and TPUUs with capsule form and between 500 and 800 mg of amoxycillin 
as an active ingredient




ok - so the query would be applied to instances in a drug database (each 
instance there is a drug descriptor)?


- thomas
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Re: SNOMED CT constraint syntax - for querying instances or terminology?

[Michael.Lawley]

Hi Thomas,

These constraints are essentially queries over the snomed definitional content 
(ie the Relationships), not queries over external data (ie not EHRs).  The 
intent is to identify sets of snomed concepts that satisfy the constraint 
criteria. These sets could be subsequently used to join against/filter records 
in an EHR/EMR.

Work is ongoing for a full featured query language to address this larger 
problem, but the expression constraint language can be used to great effect 
when combined with SQL or other database tech to query health records.

Michael

Sent from my iPhone

On 29 Sep 2015, at 11:11 PM, Thomas Beale 
> 
wrote:


The latest version of the SNOMED CT constraint language 
 proposes expressions like the 
following:

Section 6.3

To find those capsules  that have a strength between 500 and 800 mg 
(inclusive), the following expression  constraint  may be used:

<  27658006 |amoxicillin| :
46001 |has  dose form| = <<  385049006 | capsule|,
{ 15 |has basis of strength| =  ( 15 |amoxicillin only| :
15 |strength magnitude| >=  #500, 15 |strength magnitude| <= 
#800,
15 |strength unit| =  258684004 |mg|)}

The purpose of this is apparently as a query to find instances of Amoxycillin 
recorded somewhere - presumably in EHRs, or some kind of prescriptions 
database? However, the document talks of executing queries over a 'Substrate', 
defined as 'The SNOMED CT content over which an expression constraint is 
evaluated or a query is executed.'.

Elsewhere (p12) it says:

Please  note  that  the  substrate  over which  the  expression  constraint  is 
evaluated is  not  explicitly defined within the expression constraint, and 
must therefore be established by some other means. By  default,  the  assumed  
substrate  is the  set of  active  components  from  the  snapshot release  (in 
distribution normal form) of the SNOMED CT versioned edition currently loaded 
into the given tool.

It is also not clear what the query really means - is it a query for 
Amoxycillin that has been prescribed for a specific patient? For any patient in 
some cohort? Or for a medication order that has been suspended, postponed, or 
completed?

More generally, I am not clear how the one language is intended to be used 
across SNOMED CT itself (e.g. to generate intentional ref sets) and also across 
instance data. If it's the former, it can only be concept-based; if the latter, 
the query won't correspond to whatever information model is in use for the data.

How would it be used with data based on (for example) the openEHR medication 
item archetype in the UK clinical models 
CKM, shown below?




The recommendations in section 7.5 for executing the queries seem to imply that 
they are for evaluation against SNOMED CT.

There are various other oddities, but I'll leave them for later.

if anyone who is working with this can clarify, it would be most appreciated.

- thomas
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