Hi there,
I had a similar issue lately and just came up with an idea for
local/custom terminology bindings - i.e. linking at codes to external
terminologies not formally defined in UMLS or elsewhere.
My problem was to bind terms to latest version of SNOMED through which I
access from UMLS. In the Ocean Archetype Editor when you want to add a
new terminology, a list is presented (possibly taken from UMLS knowledge
sources) which contains only SNOMED CT 2002 version. So I added
SNOMED_CT manually via text editor:
ontology
terminologies_available = <"MST2", "UMLS", "SNOMED_CT">
NOTE: editor does not like spaces in term name!
And in the term bindings section I did following:
["SNOMED_CT"] = <
items = <
["at0111"] = <[SNOMED_CT::C0003461]>
["at0112"] = <[SNOMED_CT::181261002]>
["at0113"] = <[SNOMED_CT::60184004]>
The editor does not display SNOMED_CT in the combobox but only blank
line (working with enumerated text values). However you can select it
and see your bindings ;)
So custom/local terminologies can be handled this way and the
implementation will be left to developers....BUT this may result in
different implementations which may render interoperability in the long
run....
So I suggest a sub-section within ontology section where used
terminologies are declared explicitly; i.e. "umls": 2008AA version of
NLM UMLS knowledge sources. Perhaps an URI and other details can be
specified (i.e. WSDL). I think it is easier for the community to agree
on such a naming convention.
Custom local terminologies can be declared this way and you can create
terminology names for use in term/constraint bindings.Perhaps creating a
keyword (i.e. CustomTerminology) might be a good idea so that these
names do not interfere with formal names.
Cheers,
-koray atalag
--
Koray Atalag, MD, Ph.D
Clinton Bedogni Research Fellow
The University of Auckland,
Department of Computer Science,
Private Bag 92019, Auckland 1142, New Zealand
Tel: +64 (9) 373 7599 ext. 87199
Fax: +64 (9) 308 2377
Email: koray at cs.auckland.ac.nz
Ian McNicoll wrote:
> Hi Olef,
>
> As well as being bound to multiple languages, the at-codes can be
> bound to terms from external terminologies such as ICD or SNOMED. It
> is this sort of term-binding that I think mirrors what needs to be
> done in your case.
>
> The issue that I do not fully understand is how this might work with a
> locally defined terminolgy like yours, rather than a terminology
> formally registered with UMLS.
>
> Ian
>
>
> Dr Ian McNicoll
> office / fax +44(0)141 560 4657
> mobile +44 (0)775 209 7859
> skype ianmcnicoll
> ian at mcmi.co.uk <mailto:ian at mcmi.co.uk>
>
> Clinical Analyst - Ocean Informatics ian.mcnicoll at oceaninformatics.com
> <mailto:ian.mcnicoll at oceaninformatics.com>
>
> Member of BCS Primary Health Care Specialist Group ? www.phcsg.org
> <http://www.phcsg.org>
>
>
> 2008/11/26 Olof Torgersson <oloft at chalmers.se <mailto:oloft at
> chalmers.se>>
>
> Hi,
>
> Thanks for your reply. I'm aware of the at-codes and that
> archetypes can (and do) exist in multiple languages.
>
> However, this means that a term/attribute/variable ( or whatever
> you call the parents of actual data-items) have names like
> /a/b/c/d[at0033]g/h, which are not understandable for clinicians.
>
> Now imagine that you want to analyze some clinical data using
> Excel, SPSS, or some visual data mining tool. Then one does not
> want to display at-codes, and displaying the rather descriptive
> 'text'-phrases is not optimal either. It would be better to have a
> short agreed upon name.
>
> Regards
>
> Olof
>
> 25 nov 2008 kl. 23.47 skrev Hugh Leslie:
>
>> Hi Olof
>>
>> This is exactly how openEHR works. If you have a look at the
>> underlying adl for the archetype you will see that each semantic
>> element is assigned an 'at' code which is your idea of a language
>> independent term. The text and the description that is shown in
>> the tools is actually in a language based ontology section in the
>> adl and each archetype can have one or more languages in its
>> ontology. Archetypes themselves have no language primacy and
>> there are now many archetypes that have multiple languages.
>>
>> If you are using the openEHR clinical knowledge manager
>> (at www.openehr.org/knowledge <http://www.openehr.org/knowledge>)
>> then you can set the language that you want to view the archetype
>> in. The Ocean archetype editor allows you to view archetypes in
>> different languages as well and translate the archetypes as I
>> assume does the Java AE. In the Ocean editor, there is a
>> Language menu where you can add a new language or select to view
>> one already present. An example to look at is the Blood Pressure
>> archetype that already has a number of translations.
>>
>> regards Hugh
>>
>> Olof Torgersson wrote:
>>> Hi,
>>>
>>> In openEHR there are two labels 'text' and 'description' used.
>>>
>>> For instance
>>>
>>> text = "Increased bowel sounds"
>>> description="Bowel sounds are more intense than normal"
>>>
>>> In the tools I have tested 'text' is used as a label to input
>>> fields.
>>>
>>> To me it would have been more natural to have 3 items, let's say
>>> 'term', 'text' and 'description' where term could be some agreed
>>> upon language independent code and text and description are
>>> localised into different languages.
>>>
>>> I guess this has been considered, but my question then is if
>>> something like this was considered what were the reasons for
>>> discarding
>>> such an approach?
>>>
>>> Regards
>>>
>>> Olof Torgersson
>>>
>>> ---
>>> Olof Torgersson
>>>
>>> Associate Professor
>>> Department of Computer Science and Engineering
>>> Chalmers University of Technology and G?teborg University
>>> SE-412 96 G?teborg, Sweden
>>>
>>> email: oloft at chalmers.se <mailto:oloft at chalmers.se>
>>> phone: +46 31 772 54 06
>>>
>>>
>>>
>>>
>>>
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>>
>> --
>> ________________________________________________
>> Dr Hugh Leslie MBBS, Dip. Obs. RACOG, FRACGP, FACHI
>> Clinical Director
>> Ocean Informatics Pty Ltd
>> M: +61 404 033 767 E: hugh.leslie at oceaninformatics.com
>> <mailto:hugh.leslie at oceaninformatics.com> W: www.oceaninformatics.com
>> <http://www.oceaninformatics.com>
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>
> ---
> Olof Torgersson
>
> Associate Professor
> Department of Computer Science and Engineering
> Chalmers University of Technology and G?teborg University
> SE-412 96 G?teborg, Sweden
>
> email: oloft at chalmers.se <mailto:oloft at chalmers.se>
> phone: +46 31 772 54 06
>
>
>
>
>
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