subject:"RE\: Binding to multiple terminologies \/ code systems"

Re: Binding to multiple terminologies / code systems

2015-10-30 Thread Thomas Beale



Dave,

the solution to this situation is not yet 100% clear in ADL2 (it is in 
ADL1.4, as others have described). We are trying to define a cleaner way 
to represent it in ADL2, but I'm still not clear on the requirements. It 
appears that the scenario you have is that since SNOMED CT, READ and 
CTV3 are extant in the UK, coding should be allowed using any of those, 
but not by other means.


Does this apply across the whole HSCIC model library? Or do you want 
some more fine-grained control, e.g.:


 * do you want to designate certain terminologies for specific
   templates ? E.g. template A can only use SCT, but template B can use
   any of the three?
 * do you need to say on a node-by-node basis in a single template,
   e.g. this node must be coded by SCT, but this other node by say
   SCT-or-READ, and this third node, any of the 3 are allowed?

If others can clarify requirements in this area as well, it would be 
very helpful.


See here in the ADL2 draft spec 
for 
current thinking on this.


thanks

- thomas


On 29/10/2015 15:31, Barnet David (HEALTH AND SOCIAL CARE INFORMATION 
CENTRE) wrote:


All

I have a modelling issue where I’m trying to bind a single data point 
or an archetype to a choice of terminology & code systems.


The actual use case is that I’m modelling a new-born hips examination, 
and the result may be given as either a SNOMED CT concept, a Read 2 
code or a CTV3 code (for those unfamiliar with Read 2 & CTV3, they are 
code systems used (mostly) in primary care in the UK). In the actual 
instance, each code/concept will have a code system identifier to 
distinguish the actual code system used


For example, a result of “no abnormalities and no risk factors” can be 
represented as either


*SNOMED CT*



*Read2*



*CTV3*

ID



FSN



ID



Term



ID



Term

98570100100



Newborn and Infant Physical Examination Screening Programme, hip 
examination done, no abnormality and no risk factor




9OqJ1



NIPE hip, no abnor rsk fctr



XadAN



NIPE hip, no abnor rsk fctr

In the modelling tools I see you can have a choice, but I can’t see 
how the choice supports multiple terminologies. I see that it does 
support a choice of a terminology & Free text.


Is there a “standard” way of saying a data point may be represented by 
one of 3 terminologies/codes systems? Or is this something the tooling 
deliberately stops you doing?


Thanks in advance



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RE: Binding to multiple terminologies / code systems

2015-10-30 Thread Barnet David (HEALTH AND SOCIAL CARE INFORMATION CENTRE)

Thomas
For use (NHS in England) it's probably at the template level (but it would be 
good to occasionally specify at the node level).

In England there's a concerted effort to move towards a single terminology 
(SNOMED CT), but I imagine that's a long road.

In the meantime, we have a mixed economy of coding systems.

For some interoperability (such as a GP to GP communication), there is one 
coding system in use (in this case Read, but soon to be SNOMED CT). In other 
scenarios we map to a single coding system (for example in some of our HL7 
messaging specifications, for our Commissioning Data Sets). In other scenarios 
such as Public Health England's Child Health data sets (which is where the hips 
example came from), we recognise that different systems use different coding 
systems and say to send the data in the coding system used to capture the data.

So it's a very mixed picture, and the move towards SNOMED CT will increase the 
mixture in the picture. However, the nirvana of SNOMED CT across the board will 
make thing a lot easier, but is a long way in the future (should it be reached 
at all).

Regards

Dave Barnet

From: openEHR-technical [mailto:openehr-technical-boun...@lists.openehr.org] On 
Behalf Of Thomas Beale
Sent: Fri 30/10/2015 15:04
To: openehr-technical@lists.openehr.org
Subject: Re: Binding to multiple terminologies / code systems


Dave,

the solution to this situation is not yet 100% clear in ADL2 (it is in ADL1.4, 
as others have described). We are trying to define a cleaner way to represent 
it in ADL2, but I'm still not clear on the requirements. It appears that the 
scenario you have is that since SNOMED CT, READ and CTV3 are extant in the UK, 
coding should be allowed using any of those, but not by other means.

Does this apply across the whole HSCIC model library? Or do you want some more 
fine-grained control, e.g.:

 *   do you want to designate certain terminologies for specific templates ? 
E.g. template A can only use SCT, but template B can use any of the three?
 *   do you need to say on a node-by-node basis in a single template, e.g. this 
node must be coded by SCT, but this other node by say SCT-or-READ, and this 
third node, any of the 3 are allowed?

If others can clarify requirements in this area as well, it would be very 
helpful.

See here in the ADL2 draft spec 
<http://www.openehr.org/releases/AM/latest/docs/ADL2/ADL2.html#_terminology_integration>
 for current thinking on this.

thanks

- thomas

On 29/10/2015 15:31, Barnet David (HEALTH AND SOCIAL CARE INFORMATION CENTRE) 
wrote:
All
I have a modelling issue where I'm trying to bind a single data point or an 
archetype to a choice of terminology & code systems.

The actual use case is that I'm modelling a new-born hips examination, and the 
result may be given as either a SNOMED CT concept, a Read 2 code or a CTV3 code 
(for those unfamiliar with Read 2 & CTV3, they are code systems used (mostly) 
in primary care in the UK). In the actual instance, each code/concept will have 
a code system identifier to distinguish the actual code system used

For example, a result of "no abnormalities and no risk factors" can be 
represented as either

SNOMED CT

Read2

CTV3

ID

FSN

ID

Term

ID

Term

98570100100

Newborn and Infant Physical Examination Screening Programme, hip examination 
done, no abnormality and no risk factor

9OqJ1

NIPE hip, no abnor rsk fctr

XadAN

NIPE hip, no abnor rsk fctr


In the modelling tools I see you can have a choice, but I can't see how the 
choice supports multiple terminologies. I see that it does support a choice of 
a terminology & Free text.

Is there a "standard" way of saying a data point may be represented by one of 3 
terminologies/codes systems? Or is this something the tooling deliberately 
stops you doing?

Thanks in advance





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Re: Binding to multiple terminologies / code systems

2015-10-30 Thread Thomas Beale

On 30/10/2015 16:00, Barnet David (HEALTH AND SOCIAL CARE INFORMATION 
CENTRE) wrote:

Thomas

For use (NHS in England) it’s probably at the template level (but it 
would be good to occasionally specify at the node level).

just to be clear on this point, because this is the one I want to know 
about. Consider the following archetype extract:

~

definition

OBSERVATION[id1] matches {-- *Liver function test*
data matches {
HISTORY[id2] matches {
events matches {
EVENT[id3] matches {-- Any event
data matches {
ITEM_TREE[id4] matches {
items matches {
ELEMENT[id6] occurrences matches 
{0..1} matches {-- *Test name*

value matches {
DV_CODED_TEXT matches {[ac1]}
}
}
ELEMENT[id7] occurrences matches 
{0..1} matches {-- *Test status*

value matches {
DV_CODED_TEXT matches {[ac2]}
}
}
 CLUSTER[id8] occurrences matches 
{0..1} matches {-- *panel*

items matches {
ELEMENT[id6] occurrences 
matches {0..1} matches {-- *bilirubin*

value matches {
DV_QUANTITY matches 
{...}

}
}
 -- etc
}
}
   }
   }
   }
   }
   }
   }
   }

terminology
bindings
["snomed_ct"] =  <

["ac2"] =   -- 
assume SNOMED has a value set of test statuses

["id3"] =   -- SCT code for 
bilirubin

>
["loinc"] =  <

["id1"] =   -- LOINC code for 
'Liver function test'

["ac1"] =   -- assume 
LOINC has a value set of specific LFT test names (there are >1)

>

~~~

In the above, we don't need to do anything special to make sure that the 
node id1 and value set at ac1 are coded from SNOMED CT, and that id3 and 
ac2 are coded from LOINC - because the bindings don't provide for 
anything else. But if there was a binding for ["id1"] in both the 
snomed_ct and the loinc binding group then we might need a capability to 
say: on this particular OPT, I only want to allow LOINC at node id1, 
while being able to allow other nodes to still use SNOMED CT and / or 
LOINC in different permutations.

The latter is obviously more complicated to specify in a generated 
template, because now you really do have to able to mark different nodes 
as differentially subsetting their allowed bindings, for some particular 
purpose.

I'm hoping we don't need to do this, but would like to know if it is needed.

thanks

- thomas

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Re: Binding to multiple terminologies / code systems

2015-10-29 Thread Dmitry Baranov

Hi, 

Using Archetype Editor I was succeeded to bind a coded text to two terms from 
different coding systems:


ELEMENT[at1054] occurrences matches {0..1} matches {-- New Element
  name matches {
DV_TEXT matches {*}
  }
  value matches {
DV_CODED_TEXT matches {
  defining_code matches {[ac0001]}  -- New Constraints
}
  }
}

...

constraint_bindings = <
  ["LOINC"] = <
items = <
  ["ac0001"] = 
>
  >
  ["ICD10_1998"] = <
items = <
  ["ac0001"] = 
>
  >
>




-- 
Regards, Dmitry

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Re: Binding to multiple terminologies / code systems

2015-10-29 Thread Thomas Beale



The answer isn't completely simple. Some background here 
. 
If there are bindings defined for snomed_ct, read2 and ctv3 to the 
ac-code that appears in the archetype definition section, and no further 
constraint is given, the implication is that any code from any 
terminology with a binding may be used at runtime. Since this is 
normally on a value-set by value-set basis, each value set (each 
distinct ac-code) will have a binding entry only in those terminology 
groups in the binding section that make sense.


On 29/10/2015 15:31, Barnet David (HEALTH AND SOCIAL CARE INFORMATION 
CENTRE) wrote:


All

I have a modelling issue where I’m trying to bind a single data point 
or an archetype to a choice of terminology & code systems.


The actual use case is that I’m modelling a new-born hips examination, 
and the result may be given as either a SNOMED CT concept, a Read 2 
code or a CTV3 code (for those unfamiliar with Read 2 & CTV3, they are 
code systems used (mostly) in primary care in the UK). In the actual 
instance, each code/concept will have a code system identifier to 
distinguish the actual code system used


For example, a result of “no abnormalities and no risk factors” can be 
represented as either


*SNOMED CT*



*Read2*



*CTV3*

ID



FSN



ID



Term



ID



Term

98570100100



Newborn and Infant Physical Examination Screening Programme, hip 
examination done, no abnormality and no risk factor




9OqJ1



NIPE hip, no abnor rsk fctr



XadAN



NIPE hip, no abnor rsk fctr

In the modelling tools I see you can have a choice, but I can’t see 
how the choice supports multiple terminologies. I see that it does 
support a choice of a terminology & Free text.


Is there a “standard” way of saying a data point may be represented by 
one of 3 terminologies/codes systems? Or is this something the tooling 
deliberately stops you doing?


Thanks in advance

Dave Barnet
Interoperability Lead

Interoperability Specifications

Health & Social Care Information Centre

NHS in England


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Re: Binding to multiple terminologies / code systems

2015-10-29 Thread Ian McNicoll

Hi Dave,

As Thomas suggests, it does depend on whether you expect to be binding to a
single term from the terminology

e.g.

DNACPR decision in
http://clinicalmodels.org.uk/ckm/#showArchetype_1051.32.185

in which case Dmitry's advice is correct and the Archetype Editor allows
you to add bindings to
any/all of the terms via the terminology, then term-binding tab. Not the
nicest UI but you get there!!

If the target needs to be selected from a list of possible options then
Thomas's advice is appropriate. One issue is that we do not have good
industry standard ways of defining these external refset bindings, though
 it looks as if FHIR might get some traction.

Examples in this archetype
http://clinicalmodels.org.uk/ckm/#showArchetype_1051.32.4

Ian


Dr Ian McNicoll
mobile +44 (0)775 209 7859
office +44 (0)1536 414994
skype: ianmcnicoll
email: i...@freshehr.com
twitter: @ianmcnicoll

Co-Chair, openEHR Foundation ian.mcnic...@openehr.org
Director, freshEHR Clinical Informatics Ltd.
Director, HANDIHealth CIC
Hon. Senior Research Associate, CHIME, UCL

On 29 October 2015 at 18:24, Thomas Beale  wrote:

>
> The answer isn't completely simple. Some background here
> .
> If there are bindings defined for snomed_ct, read2 and ctv3 to the ac-code
> that appears in the archetype definition section, and no further constraint
> is given, the implication is that any code from any terminology with a
> binding may be used at runtime. Since this is normally on a value-set by
> value-set basis, each value set (each distinct ac-code) will have a binding
> entry only in those terminology groups in the binding section that make
> sense.
>
> On 29/10/2015 15:31, Barnet David (HEALTH AND SOCIAL CARE INFORMATION
> CENTRE) wrote:
>
> All
>
> I have a modelling issue where I’m trying to bind a single data point or
> an archetype to a choice of terminology & code systems.
>
>
>
> The actual use case is that I’m modelling a new-born hips examination, and
> the result may be given as either a SNOMED CT concept, a Read 2 code or a
> CTV3 code (for those unfamiliar with Read 2 & CTV3, they are code systems
> used (mostly) in primary care in the UK). In the actual instance, each
> code/concept will have a code system identifier to distinguish the actual
> code system used
>
>
>
> For example, a result of “no abnormalities and no risk factors” can be
> represented as either
>
>
>
> *SNOMED CT*
>
> *Read2*
>
> *CTV3*
>
> ID
>
> FSN
>
> ID
>
> Term
>
> ID
>
> Term
>
> 98570100100
>
> Newborn and Infant Physical Examination Screening Programme, hip
> examination done, no abnormality and no risk factor
>
> 9OqJ1
>
> NIPE hip, no abnor rsk fctr
>
> XadAN
>
> NIPE hip, no abnor rsk fctr
>
>
>
> In the modelling tools I see you can have a choice, but I can’t see how
> the choice supports multiple terminologies. I see that it does support a
> choice of a terminology & Free text.
>
>
>
> Is there a “standard” way of saying a data point may be represented by one
> of 3 terminologies/codes systems? Or is this something the tooling
> deliberately stops you doing?
>
>
>
> Thanks in advance
>
>
>
> Dave Barnet
> Interoperability Lead
>
> Interoperability Specifications
>
> Health & Social Care Information Centre
>
> NHS in England
>
>
>
>
> ___
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> openEHR-technical@lists.openehr.org
>
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>
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Re: Binding to multiple terminologies / code systems

2015-10-29 Thread Heath Frankel

It should also be noted that normally constraints on which terminologies can be 
used in a particular implementation is done in a template. This can be done on 
the existing DV_TEXT definition or on a DV_CODED_TEXT constraint. This can be 
expressed in the template designer, again not the best UI but you get there... 
Not sure that archetype constraint bindings help in this step.

Regards

Heath

On 30 Oct 2015, at 5:37 am, Ian McNicoll 
> wrote:

Hi Dave,

As Thomas suggests, it does depend on whether you expect to be binding to a 
single term from the terminology

e.g.

DNACPR decision in http://clinicalmodels.org.uk/ckm/#showArchetype_1051.32.185

in which case Dmitry's advice is correct and the Archetype Editor allows you to 
add bindings to
any/all of the terms via the terminology, then term-binding tab. Not the nicest 
UI but you get there!!

If the target needs to be selected from a list of possible options then 
Thomas's advice is appropriate. One issue is that we do not have good industry 
standard ways of defining these external refset bindings, though  it looks as 
if FHIR might get some traction.

Examples in this archetype 
http://clinicalmodels.org.uk/ckm/#showArchetype_1051.32.4

Ian

Dr Ian McNicoll
mobile +44 (0)775 209 7859
office +44 (0)1536 414994
skype: ianmcnicoll
email: i...@freshehr.com
twitter: @ianmcnicoll

[https://docs.google.com/uc?id=0BzLo3mNUvbAjT2R5Sm1DdFZYTU0=download]
Co-Chair, openEHR Foundation 
ian.mcnic...@openehr.org
Director, freshEHR Clinical Informatics Ltd.
Director, HANDIHealth CIC
Hon. Senior Research Associate, CHIME, UCL

On 29 October 2015 at 18:24, Thomas Beale 
> wrote:

The answer isn't completely simple. Some background 
here.
 If there are bindings defined for snomed_ct, read2 and ctv3 to the ac-code 
that appears in the archetype definition section, and no further constraint is 
given, the implication is that any code from any terminology with a binding may 
be used at runtime. Since this is normally on a value-set by value-set basis, 
each value set (each distinct ac-code) will have a binding entry only in those 
terminology groups in the binding section that make sense.

On 29/10/2015 15:31, Barnet David (HEALTH AND SOCIAL CARE INFORMATION CENTRE) 
wrote:
All
I have a modelling issue where I’m trying to bind a single data point or an 
archetype to a choice of terminology & code systems.

The actual use case is that I’m modelling a new-born hips examination, and the 
result may be given as either a SNOMED CT concept, a Read 2 code or a CTV3 code 
(for those unfamiliar with Read 2 & CTV3, they are code systems used (mostly) 
in primary care in the UK). In the actual instance, each code/concept will have 
a code system identifier to distinguish the actual code system used

For example, a result of “no abnormalities and no risk factors” can be 
represented as either

SNOMED CT

Read2

CTV3

ID

FSN

ID

Term

ID

Term

98570100100

Newborn and Infant Physical Examination Screening Programme, hip examination 
done, no abnormality and no risk factor

9OqJ1

NIPE hip, no abnor rsk fctr

XadAN

NIPE hip, no abnor rsk fctr

In the modelling tools I see you can have a choice, but I can’t see how the 
choice supports multiple terminologies. I see that it does support a choice of 
a terminology & Free text.

Is there a “standard” way of saying a data point may be represented by one of 3 
terminologies/codes systems? Or is this something the tooling deliberately 
stops you doing?

Thanks in advance

Dave Barnet
Interoperability Lead
Interoperability Specifications
Health & Social Care Information Centre
NHS in England

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Re: Binding to multiple terminologies / code systems

RE: Binding to multiple terminologies / code systems

Re: Binding to multiple terminologies / code systems

Re: Binding to multiple terminologies / code systems

Re: Binding to multiple terminologies / code systems

Re: Binding to multiple terminologies / code systems

Re: Binding to multiple terminologies / code systems

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