Texts about transforming between openEHR and other formalisms

[Koray Atalag]

Hi All, reposting this as I just noticed it didn?t get thru list server.

Basically I?ve recently updated an openEHR bibliography list on 
Zoterohttps://www.zotero.org/groups/openehr which I?ve been curating for a 
while. For those of you who use it Zotero (open source and plug-in to Firefox) 
is clearly the best! My PhD student and I can manage entries ? if you are an 
expert Zotero user and an academician and interested in supporting its curation 
please contact me and I?ll add you to the group who can add/edit citations 
(with full text access). Unfortunately we cannot share full text publicly.


Cheers,

-koray

From: Koray Atalag
Sent: Friday, 26 September 2014 9:58 a.m.
To: For openEHR technical discussions
Cc: For openEHR clinical discussions
Subject: RE: Texts about transforming between openEHR and other formalisms


Thanks Diego - that's an impressive list.



This reminded me something I started quite a few years ago - an online up to 
date bibliography of openEHR (https://www.zotero.org/groups/openehr) and 
closely related papers. I used the open source Zotero (http://zotero.org) which 
links to my browser plug-in (you can add while you browse, fantastic sensing 
and resolving of metadata and has word plug-in to cite and create reference 
list as well) so I could keep on adding new stuff as I find but also let the 
community grow the list as well. Much better than personal effort to keep up to 
date! As I remember there were a few constraints and inconveniences at that 
time and I'll see if it is any better now - but ultimately I think we should 
look at maintaining such a list and make available from openEHR website too.



Any appetite / volunteers? Obviously we can't let everyone write access - it'll 
have to be a few of us academics to do the QA too.



Cheers,



-koray





-Original Message-
From: openEHR-technical [mailto:openehr-technical-boun...@lists.openehr.org] On 
Behalf Of Diego Bosc?
Sent: Thursday, 25 September 2014 8:51 p.m.
To: For openEHR technical discussions
Subject: Re: Texts about transforming between openEHR and other formalisms



I have the same doubts as Ian about which kinds of transformations you are 
looking for, so I'll give you a summary :)





Here we have done several works regarding data instance transformation based on 
archetypes:



- Maldonado, J. A., Moner, D., Tom?s, D., ?ngulo, C., Robles, M.,  Fern?ndez, 
J. T. (2007). Framework for clinical data standardization based on archetypes. 
Studies in health technology and informatics, 129(1), 454.



- Moner, D., Maldonado, J. A., Bosca, D., Fern?ndez, J. T., Angulo, C., Crespo, 
P., ...  Robles, M. (2006, August). Archetype-based semantic integration and 
standardization of clinical data. In Engineering in Medicine and Biology 
Society, 2006. EMBS'06. 28th Annual International Conference of the IEEE (pp. 
5141-5144). IEEE.



- Moner, D., Maldonado, J. A., Bosc?, D., Angulo, C., Robles, M., P?rez, D.,  
Serrano, P. (2010, May). CEN EN13606 normalisation framework implementation 
experiences. In Seamless Care, Safe Care: The Challenges of Interoperability 
and Patient Safety in Health Care:

Proceedings of the EFMI Special Topic Conference, June 2-4, 2010, Reykjavik, 
Iceland (Vol. 155, p. 136). IOS Press.



- Maldonado, J. A., Moner, D., Bosca, D., Angulo, C., Marco, L., Reig, E.,  
Robles, M. (2011, July). Concept-based exchange of healthcare

information: The LinkEHR approach. In Healthcare Informatics, Imaging and 
Systems Biology (HISB), 2011 First IEEE International Conference on (pp. 
150-157). IEEE.



- Mart?nez Costa, C., Men?rguez-Tortosa, M.,  Fern?ndez-Breis, J. T.

(2011). Clinical data interoperability based on archetype transformation. 
Journal of biomedical informatics, 44(5), 869-880.



- Moner, D., Moreno, A., Maldonado, J. A., Robles, M.,  Parra, C.

(2012, August). Using archetypes for defining CDA templates. In MIE (pp. 53-57).



- Moner D. LinkEHR Studio: a tool for archetype-based data transformations. 
Arctic Conference 2014

(http://vimeo.com/channels/764149)





Model transformations:



- Mart?nez-Costa, C., Men?rguez-Tortosa, M.,  Fern?ndez-Breis, J. T.

(2010). An approach for the semantic interoperability of ISO EN 13606 and 
OpenEHR archetypes. Journal of biomedical informatics, 43(5), 736-746.



- Mart?nez-Costa, C., Bosca, D., Legaz-Garc?a, M. C., Tao, C., Fern?ndez, B. 
J., Schulz, S.,  Chute, C. G. (2012). Isosemantic Rendering of Clinical 
Information Using Formal Ontologies and RDF.

Studies in health technology and informatics, 192, 1085-1085.



- Lezcano, L., Sicilia, M. A.,  Rodr?guez-Solano, C. (2011).

Integrating reasoning and clinical archetypes using OWL ontologies and SWRL 
rules. Journal of biomedical informatics, 44(2), 343-353.



- Detailed Clinical Models to facilitate inter-standard interoperability of 
data types. Diego Bosc?, Jos? Alberto Maldonado, David Moner, Montserrat 
Robles. XXIII International Conference of the European Federation

Texts about transforming between openEHR and other formalisms

[Bakke, Silje Ljosland]

Thanks ?ystein! I was primarily looking for something on a more specific and 
practical level, but I guess Rector is a good place to start.

Kind regards,
Silje Ljosland Bakke
Coordinator, National Editorial Board for Archetypes, National ICT Norway
Adviser, RD dept, E-health section, Bergen Hospital Trust
Tel. +47 40203298

Fra: openEHR-technical [mailto:openehr-technical-bounces at lists.openehr.org] 
P? vegne av ?ystein Nytr?
Sendt: 24. september 2014 20:59
Til: For openEHR technical discussions
Emne: Re: Texts about transforming between openEHR and other formalisms

24. sep. 2014 kl. 18.01 skrev Bakke, Silje Ljosland silje.ljosland.bakke at 
helse-bergen.nomailto:silje.ljosland.bakke at helse-bergen.no:


Hi,

I'm wondering if anyone could point me to any publically available texts about 
transforming archetypes (and templates) from openEHR to other formalisms. 
Academic publications exploring the (im)possibilities of automatic 
transformation would be ideal.


A highly recommended and succinct article about the distinctions, relationships 
and transformations between archetypes, frames, templates and
semantically tractable formalisms is: Alan Rector's: Axioms  Templates: 
Distinctions  Transformations amongst Ontologies, Frames,  Information 
Models .
His way of clearing up the terminology about (my words here...) information 
model (in the computer), templates (presentations for humans)
and domain knowledge (boundaries of reality) should be required reading for 
anyone working on domain modelling.
Look into the citations for more background. Available freely here: 
http://dl.acm.org/citation.cfm?id=2479840

(Archetypes are essentially just another template/frame/OO-inspired modelling 
convention. And yes, Alan Rector is  THE authority on the subject matter.)

Best regards,
--- ?ystein Nytr?

---
Inst. for datateknikk  og info.vitenskap | Dept. of computer and info. science
IDI, NTNU, NO-7491 TRONDHEIM, Norway
tel +47 73594459, mob +47 91897606



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Texts about transforming between openEHR and other formalisms

[Øystein Nytrø]

24. sep. 2014 kl. 23.32 skrev Bakke, Silje Ljosland silje.ljosland.bakke at 
helse-bergen.no:

 Thanks ?ystein! I was primarily looking for something on a more specific and 
 practical level, but I guess Rector is a good place to start.


Well, the article is both specific and practical. These are fundamental issues 
relevant for all information and knowledge modelling.

Sorry that the pointer was paywalled. 
Try the version 
https://www.escholar.manchester.ac.uk/api/datastream?publicationPid=uk-ac-man-scw:201196datastreamId=FULL-TEXT.PDF
at Alan Rectors home page: http://www.cs.man.ac.uk/~rector/home_page_rector/

Essentially, transformation is difficult/meaningless if
 a) the representations are about different domains of discourse (data 
model, interface model, reality model)
 (identical labels for different purposes in different representations 
= future pain)
 b) semantics are informal or undefined.

Hi ho,
--- ?ystein N.


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Texts about transforming between openEHR and other formalisms

[Ian McNicoll]

Hi Silje,

Di you mean transforms from openEHR archetypes to other design-time
formalisms e.g 13606 archetypes, CDA templates, FHIR resources?

The work done by David Moner in LinkEhr and academic work by Cati Martinez
should be helpful

http://person.hst.aau.dk/ska/MIE2009/papers/MIE2009p0260.pdf

Also NEHTA used the Toolchain features in CKM ( chained XSL transforms) to
generate CDA templates from openEHR artefacts.

OTOH perhaps you meant transforming runtime data, based on openEHR
archetypes e.g to a CDA document. This has been done by many companies in
many places but I am not sure any of it is freely available (yet).

Would any of the openEHR vendors be prepared to share their some of their
transform source for educational purposes?

Ian



On 24 September 2014 17:01, Bakke, Silje Ljosland 
silje.ljosland.bakke at helse-bergen.no wrote:

 Hi,



 I?m wondering if anyone could point me to any publically available texts
 about transforming archetypes (and templates) from openEHR to other
 formalisms. Academic publications exploring the (im)possibilities of
 automatic transformation would be ideal.



 Kind regards,
 *Silje Ljosland Bakke*

 Coordinator, National Editorial Board for Archetypes, National ICT Norway
 Adviser, RD dept, E-health section, Bergen Hospital Trust

 Tel. +47 40203298

 ___
 openEHR-technical mailing list
 openEHR-technical at lists.openehr.org

 http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org




-- 
Dr Ian McNicoll
office +44 (0)1536 414 994
fax +44 (0)1536 516317
mobile +44 (0)775 209 7859
skype ianmcnicoll
ian.mcnicoll at oceaninformatics.com

Clinical Modelling Consultant, Ocean Informatics, UK
Director openEHR Foundation  www.openehr.org/knowledge
Honorary Senior Research Associate, CHIME, UCL
SCIMP Working Group, NHS Scotland
BCS Primary Health Care  www.phcsg.org
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Texts about transforming between openEHR and other formalisms

[Diego Boscá]

I have the same doubts as Ian about which kinds of transformations you
are looking for, so I'll give you a summary :)


Here we have done several works regarding data instance transformation
based on archetypes:

- Maldonado, J. A., Moner, D., Tom?s, D., ?ngulo, C., Robles, M., 
Fern?ndez, J. T. (2007). Framework for clinical data standardization
based on archetypes. Studies in health technology and informatics,
129(1), 454.

- Moner, D., Maldonado, J. A., Bosca, D., Fern?ndez, J. T., Angulo,
C., Crespo, P., ...  Robles, M. (2006, August). Archetype-based
semantic integration and standardization of clinical data. In
Engineering in Medicine and Biology Society, 2006. EMBS'06. 28th
Annual International Conference of the IEEE (pp. 5141-5144). IEEE.

- Moner, D., Maldonado, J. A., Bosc?, D., Angulo, C., Robles, M.,
P?rez, D.,  Serrano, P. (2010, May). CEN EN13606 normalisation
framework implementation experiences. In Seamless Care, Safe Care: The
Challenges of Interoperability and Patient Safety in Health Care:
Proceedings of the EFMI Special Topic Conference, June 2-4, 2010,
Reykjavik, Iceland (Vol. 155, p. 136). IOS Press.

- Maldonado, J. A., Moner, D., Bosca, D., Angulo, C., Marco, L., Reig,
E.,  Robles, M. (2011, July). Concept-based exchange of healthcare
information: The LinkEHR approach. In Healthcare Informatics, Imaging
and Systems Biology (HISB), 2011 First IEEE International Conference
on (pp. 150-157). IEEE.

- Mart?nez Costa, C., Men?rguez-Tortosa, M.,  Fern?ndez-Breis, J. T.
(2011). Clinical data interoperability based on archetype
transformation. Journal of biomedical informatics, 44(5), 869-880.

- Moner, D., Moreno, A., Maldonado, J. A., Robles, M.,  Parra, C.
(2012, August). Using archetypes for defining CDA templates. In MIE
(pp. 53-57).

- Moner D. LinkEHR Studio: a tool for archetype-based data
transformations. Arctic Conference 2014
(http://vimeo.com/channels/764149)


Model transformations:

- Mart?nez-Costa, C., Men?rguez-Tortosa, M.,  Fern?ndez-Breis, J. T.
(2010). An approach for the semantic interoperability of ISO EN 13606
and OpenEHR archetypes. Journal of biomedical informatics, 43(5),
736-746.

- Mart?nez-Costa, C., Bosca, D., Legaz-Garc?a, M. C., Tao, C.,
Fern?ndez, B. J., Schulz, S.,  Chute, C. G. (2012). Isosemantic
Rendering of Clinical Information Using Formal Ontologies and RDF.
Studies in health technology and informatics, 192, 1085-1085.

- Lezcano, L., Sicilia, M. A.,  Rodr?guez-Solano, C. (2011).
Integrating reasoning and clinical archetypes using OWL ontologies and
SWRL rules. Journal of biomedical informatics, 44(2), 343-353.

- Detailed Clinical Models to facilitate inter-standard
interoperability of data types. Diego Bosc?, Jos? Alberto Maldonado,
David Moner, Montserrat Robles. XXIII International Conference of the
European Federation for Medical Informatics (MIE 2011), Oslo;
Proceedings (2011)


GUI

- Men?rguez-Tortosa, M., Mart?nez-Costa, C.,  Fern?ndez-Breis, J. T.
(2012). A generative tool for building health applications driven by
iso 13606 archetypes. Journal of medical systems, 36(5), 3063-3075.

- Brass, A., Moner, D., Hildebrand, C.,  Robles, M. (2010).
Standardized and flexible health data management with an archetype
driven EHR system (EHRflex). Studies in health technology and
informatics, 155, 212.


One about combining all the above

- Maldonado, J. A., Costa, C. M., Moner, D., Men?rguez-Tortosa, M.,
Bosc?, D., Mi?arro Gim?nez, J. A., ...  Robles, M. (2012). Using the
ResearchEHR platform to facilitate the practical application of the
EHR standards. Journal of biomedical informatics, 45(4), 746-762.


Transformations for the use of archetypes for clinical guidelines

- Marcos, M., Maldonado, J. A., Mart?nez-Salvador, B., Moner, D.,
Bosc?, D.,  Robles, M. (2011). An archetype-based solution for the
interoperability of computerised guidelines and electronic health
records. In Artificial Intelligence in Medicine (pp. 276-285).
Springer Berlin Heidelberg.

(there are plenty of papers on the modeling of clinical guidelines in openEHR)


Transformations of archetypes for the validation of clinical data

- Pfeiffer, Klaus, Georg Duftschmid, and Christoph Rinner. ?Validating
EHR Documents: Automatic Schematron Generation Using Archetypes.?
Studies in Health Technology and Informatics 198 (2014): 101?7.

We are currently working on a paper for the generation of
implementation guides from archetypes. Archetypes are transformed into
NRL (natural rules language), Schematron and other validation
artifacts


If you don't have access to any of the above papers I can probably
provide you with preprints.

2014-09-25 9:42 GMT+02:00 Ian McNicoll ian.mcnicoll at oceaninformatics.com:
 Hi Silje,

 Di you mean transforms from openEHR archetypes to other design-time
 formalisms e.g 13606 archetypes, CDA templates, FHIR resources?

 The work done by David Moner in LinkEhr and academic work by Cati Martinez
 should be helpful

 

Texts about transforming between openEHR and other formalisms

[Gerard Freriks]

Hi,

At last I can use copies for my own collection of articles


Gerard Freriks
+31 620347088
gfrer at luna.nl

On 25 sep. 2014, at 10:50, Diego Bosc? yampeku at gmail.com wrote:

 I have the same doubts as Ian about which kinds of transformations you
 are looking for, so I'll give you a summary :)
 
 
 Here we have done several works regarding data instance transformation
 based on archetypes:
 
 - Maldonado, J. A., Moner, D., Tom?s, D., ?ngulo, C., Robles, M., 
 Fern?ndez, J. T. (2007). Framework for clinical data standardization
 based on archetypes. Studies in health technology and informatics,
 129(1), 454.
 
 - Moner, D., Maldonado, J. A., Bosca, D., Fern?ndez, J. T., Angulo,
 C., Crespo, P., ...  Robles, M. (2006, August). Archetype-based
 semantic integration and standardization of clinical data. In
 Engineering in Medicine and Biology Society, 2006. EMBS'06. 28th
 Annual International Conference of the IEEE (pp. 5141-5144). IEEE.
 
 - Moner, D., Maldonado, J. A., Bosc?, D., Angulo, C., Robles, M.,
 P?rez, D.,  Serrano, P. (2010, May). CEN EN13606 normalisation
 framework implementation experiences. In Seamless Care, Safe Care: The
 Challenges of Interoperability and Patient Safety in Health Care:
 Proceedings of the EFMI Special Topic Conference, June 2-4, 2010,
 Reykjavik, Iceland (Vol. 155, p. 136). IOS Press.
 
 - Maldonado, J. A., Moner, D., Bosca, D., Angulo, C., Marco, L., Reig,
 E.,  Robles, M. (2011, July). Concept-based exchange of healthcare
 information: The LinkEHR approach. In Healthcare Informatics, Imaging
 and Systems Biology (HISB), 2011 First IEEE International Conference
 on (pp. 150-157). IEEE.
 
 - Mart?nez Costa, C., Men?rguez-Tortosa, M.,  Fern?ndez-Breis, J. T.
 (2011). Clinical data interoperability based on archetype
 transformation. Journal of biomedical informatics, 44(5), 869-880.
 
 - Moner, D., Moreno, A., Maldonado, J. A., Robles, M.,  Parra, C.
 (2012, August). Using archetypes for defining CDA templates. In MIE
 (pp. 53-57).
 
 - Moner D. LinkEHR Studio: a tool for archetype-based data
 transformations. Arctic Conference 2014
 (http://vimeo.com/channels/764149)
 
 
 Model transformations:
 
 - Mart?nez-Costa, C., Men?rguez-Tortosa, M.,  Fern?ndez-Breis, J. T.
 (2010). An approach for the semantic interoperability of ISO EN 13606
 and OpenEHR archetypes. Journal of biomedical informatics, 43(5),
 736-746.
 
 - Mart?nez-Costa, C., Bosca, D., Legaz-Garc?a, M. C., Tao, C.,
 Fern?ndez, B. J., Schulz, S.,  Chute, C. G. (2012). Isosemantic
 Rendering of Clinical Information Using Formal Ontologies and RDF.
 Studies in health technology and informatics, 192, 1085-1085.
 
 - Lezcano, L., Sicilia, M. A.,  Rodr?guez-Solano, C. (2011).
 Integrating reasoning and clinical archetypes using OWL ontologies and
 SWRL rules. Journal of biomedical informatics, 44(2), 343-353.
 
 - Detailed Clinical Models to facilitate inter-standard
 interoperability of data types. Diego Bosc?, Jos? Alberto Maldonado,
 David Moner, Montserrat Robles. XXIII International Conference of the
 European Federation for Medical Informatics (MIE 2011), Oslo;
 Proceedings (2011)
 
 
 GUI
 
 - Men?rguez-Tortosa, M., Mart?nez-Costa, C.,  Fern?ndez-Breis, J. T.
 (2012). A generative tool for building health applications driven by
 iso 13606 archetypes. Journal of medical systems, 36(5), 3063-3075.
 
 - Brass, A., Moner, D., Hildebrand, C.,  Robles, M. (2010).
 Standardized and flexible health data management with an archetype
 driven EHR system (EHRflex). Studies in health technology and
 informatics, 155, 212.
 
 
 One about combining all the above
 
 - Maldonado, J. A., Costa, C. M., Moner, D., Men?rguez-Tortosa, M.,
 Bosc?, D., Mi?arro Gim?nez, J. A., ...  Robles, M. (2012). Using the
 ResearchEHR platform to facilitate the practical application of the
 EHR standards. Journal of biomedical informatics, 45(4), 746-762.
 
 
 Transformations for the use of archetypes for clinical guidelines
 
 - Marcos, M., Maldonado, J. A., Mart?nez-Salvador, B., Moner, D.,
 Bosc?, D.,  Robles, M. (2011). An archetype-based solution for the
 interoperability of computerised guidelines and electronic health
 records. In Artificial Intelligence in Medicine (pp. 276-285).
 Springer Berlin Heidelberg.
 
 (there are plenty of papers on the modeling of clinical guidelines in openEHR)
 
 
 Transformations of archetypes for the validation of clinical data
 
 - Pfeiffer, Klaus, Georg Duftschmid, and Christoph Rinner. ?Validating
 EHR Documents: Automatic Schematron Generation Using Archetypes.?
 Studies in Health Technology and Informatics 198 (2014): 101?7.
 
 We are currently working on a paper for the generation of
 implementation guides from archetypes. Archetypes are transformed into
 NRL (natural rules language), Schematron and other validation
 artifacts
 
 
 If you don't have access to any of the above papers I can probably
 provide you with preprints.

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Texts about transforming between openEHR and other formalisms

[Bakke, Silje Ljosland]

Hi,

I'm wondering if anyone could point me to any publically available texts about 
transforming archetypes (and templates) from openEHR to other formalisms. 
Academic publications exploring the (im)possibilities of automatic 
transformation would be ideal.

Kind regards,
Silje Ljosland Bakke
Coordinator, National Editorial Board for Archetypes, National ICT Norway
Adviser, RD dept, E-health section, Bergen Hospital Trust
Tel. +47 40203298
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Texts about transforming between openEHR and other formalisms

[Øystein Nytrø]

24. sep. 2014 kl. 18.01 skrev Bakke, Silje Ljosland silje.ljosland.bakke at 
helse-bergen.no:

 Hi,
  
 I?m wondering if anyone could point me to any publically available texts 
 about transforming archetypes (and templates) from openEHR to other 
 formalisms. Academic publications exploring the (im)possibilities of 
 automatic transformation would be ideal.
  

A highly recommended and succinct article about the distinctions, relationships 
and transformations between archetypes, frames, templates and 
semantically tractable formalisms is: Alan Rector's: Axioms  Templates: 
Distinctions  Transformations amongst Ontologies, Frames,  Information 
Models .
His way of clearing up the terminology about (my words here...) information 
model (in the computer), templates (presentations for humans)
and domain knowledge (boundaries of reality) should be required reading for 
anyone working on domain modelling.
Look into the citations for more background. Available freely here: 
http://dl.acm.org/citation.cfm?id=2479840

(Archetypes are essentially just another template/frame/OO-inspired modelling 
convention. And yes, Alan Rector is  THE authority on the subject matter.)

Best regards,
--- ?ystein Nytr?

---
Inst. for datateknikk  og info.vitenskap | Dept. of computer and info. science
IDI, NTNU, NO-7491 TRONDHEIM, Norway
tel +47 73594459, mob +47 91897606



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