LinkEHR-Ed - IBIME - Biomedical Informatics Group
Contents
1. g un La hi H a E ul S in in uf in on units lt mm Hg gt magnitude lt 0 0 1000 0 gt Precision lt O gt Capture 15 The ADL edition view The main edition process is done at the definition branch of the archetype tree By clicking on any node a form 1s shown in the details view with the editable information of the node This form will depend on the type of node e Attribute There are views for editing properties of Single and Multiple attributes archetype_node_id ANY ALLOWED MANDATORY C_Multi_Attribute content ANY ALLOWED MANDATORY LJ ordered Unique Aa Min 0 aga Max Unbounded Capture 16 Single and multiple attributes view 18 e Complex Object Occurrences of complex objects can be modified through their respective form Their ontology information term definition and term binding can also be edited from this form ome Cb Ir OBSERVATION LJ ANY ALLOWED Occurrences pa Min 1 3 Max E Unbounded Text Blood pressure Description the measurement by any means invasive or noninvasive of systemic arterial blood pressure which is deemed to represent the actual systemic blood pressure NOMED CT 2003 16302000 Capture 17 CComplexObject edition view e Internal Reference When an internal reference is created a list of the available target nodes of the same reference model type is provided You can change the target node at a2. Capture 5 The entities of OpenEHR reference model Now we can check that the imported reference model has been included by trying to create a new archetype Push Archetype New and the window of capture 6 will appear See section 5 for more details 10 11 Archetype Editor o The entity cannot be ommited Organization OpenEHR Ww Reference Model EHR Entity Concept Language COMPOSITION ELEMENT Capture 6 The new archetype wizard with the OpenEHR reference model included Adding CEN EN13606 reference model to LinkEHR Ed In the same way we have added the OpenEHR reference model we can add the CEN EN13606 reference model to LinkEHR Ed So the first page will be as shown on the capture 7 NOTE There is no official XML Schema for CEN EN13606 We have developed our own schema and it is available through the LinkEHR ED project webpage Import reference model Set an organization a name and the XML Schema files from where the new reference model will be created Capture 7 Importing CEN EN 13606 In the same way as before we select the reference model entities to be included and push finish The entities needed for EN13606 are shown at capture 8 12 5 13 Include reference model entities Select the entities to be induded The entities are displayed in complexity order Not included Induded ATTESTATION_INFO N COMPOSITION QUANTITY RANGE SECTION IVL ENTRY AUDIT_INFO 3
3. Data transformations may be expressed in a specific data transformation language such as XQuery or by using a general purpose language as Java Since the health data to be made public resides in the underlying data sources it is necessary to define some kind of mapping information that links entities described in the archetype object nodes and attributes to data elements in data repositories e g elements and attributes in the case of XML documents tables and attributes in the case of relational data sources We use the term integration archetype to denote an archetype for which a mapping specification to a set of data sources has been defined 1 e Integration archetype archetype mapping specification An integration archetype can be considered to be a view that provides abstraction in interfacing between the data sources that hold the data to be shared and the reference model used to communicate these data in the form of standardized EHR extracts It is necessary to remark that there exits a one to many relationship between archetypes and integration archetypes Given an archetype there may be different mappings one for each different setting that wishes to use the archetype to describe and share its data LinkEHR Ed is a visual tool for defining integration archetypes Although LinkEHR Ed is oriented to the construction of integration archetypes it may Operate as a pure archetype editor It can load ADL files and generate both ADL
4. _ CLUSTER RTO 3 FOLDER FUNCTIONAL ROLE ELEMENT ED i ORD ST CODED TEXT SIMPLE_TEXT LINK PQ EIVL FIVL Entity complexity Less complexity j _ _ More complexity Capture 8 Reference model entities for CEN EN13606 Creating a new archetype To create a new archetype we only have to push the New Archetype button of the toolbar or the menu Archetype New and a wizard shown at capture 6 will be opened After selecting the organization reference model entity concept and language a new and empty archetype will be loaded and ready for being edited capture 9 l gt LinkEHR Ed Integration Archetype Editor Archetype Edit Reference Model Datasources Help teh ve a 2 A Archetype Tree t amp ae A Archetype A CEN EN 13606 COMPOSITION laboratory_test v1 ARCHETYPE A I Definition te COMPOSITION at0000 1 Header Language A Identifier CEN EN 13606 COMPOSITION laboratory_test v1 Ontology Specializes Concept laboratory_test Lifecycle State Draft v Version 1 Original Language EN Resource Package URI Archetype Package URI Details Copyright Use Misuse 6 14 Original Resource URI Parsing completed Capture 9 LinkEHR Ed with a new archetype created Opening an archetype This process 1s very straightforward By pushing the Open button on the toolbar or the menu Archetype Open a typical system open dialog will be sh
5. 0 5 1 to LinkEHR Ed v0 5 4 Minor changes and bugs resolved LinkEHR Ed v0 8 Current release includes the integration archetypes feature Only for XML data sources Future versions LinkEHR Ed v0 9 This release will include support for relational data sources LinkEHR Ed v1 First final and usable version of the complete LinkEHR Ed 4 What is LinkEHR Ed LinkEHR Ed is a visual tool implemented in Java under the Eclipse platform which allows the edition of archetypes based on different reference models the specification of mappings between archetypes and data sources and the semi automatic generation of data conversion scripts which translate unnormalized data into XML documents which conform to the reference model and at the same time satisfy the data constraints imposed by archetypes LinkEHR Ed explores the use of archetypes as a means to achieve standardization and semantic data integration of distributed health data The main objectives are twofold Firstly in the context of data integration to use of archetypes as a semantic layer over the data repositories whose contents need to be integrated and exchanged associating them with formal semantics As aforementioned the main purpose of archetypes is to describe information in the form of a set of machine processable domain concept definitions based on a reference model Therefore archetypes may act as semantic descriptions that capture the information contents of heterogeneou
6. In the next wizard page will appear the list of entities available to be generated The list is filled with the entities in complexity order as it is likely that the more complex entities will be the ones basic to that model also called Business Objects If a needed entity does not appear in the list you can move the slider in order to reveal less complex entities They are hidden at first to simplify the whole process When you have all the desired entities visible you only have to select them and click on the arrow to the right This will show the selected entities on the included list NOTE Included entities will be the only ones available as basis for creating new archetypes at the New archetype dialog When at least one entity 1s included you can finish the importation process Capture 5 shows the entities of OpenEHR reference model Include reference model entities Select the entities to be included The entities are displayed in complexity order Not induded Induded AAA HISTORY ee F INTERVAL EVENT p SECTION POINT EVENT OBSERVATION EVENT CONTEXT ACTION ACTIVITY INSTRUCTION INSTRUCTION DETA EVALUATION items ITEM_TABLE FEEDER AUDIT ITEM SINGLE version TTEM_ TREE ATTESTATION ITEM LIST FEEDER AUDIT DET ADMIN ENTRY AUDIT DETAILS CLUSTER DY_DATE_TIME ELEMENT OY TEMPORAL PARTICIPATION rr a M e me ee A A o man Entity complexity Less complexity i More complexity Cancel
7. LinkEHR Ed Archetype Editor v0 8 User s Manual Copyright 2005 2008 Biomedical Informatics Group IBIME ITACA Institute Universidad Polit cnica de Valencia 1 About us The Biomedical Informatics IBIME area of the Institute for the Applications of Advanced Information and Communication Technologies ITACA consists of 20 members and 1t is coordinated by Ph D Montserrat Robles Viejo TACA is a research and development centre of the Universidad Polit cnica de Valencia UPV Spain whose purpose 1s to promote and carry out research technological development and transference of results in the field of information and communication technologies The research of IBIME ITACA is concerned with the use and development of methods and tools for the acquisition processing and management of biomedical data and knowledge The research is characterised by its multidisciplinarity and close linkage with health professional and institutions IBIME collaborates with several national and international groups working on bioinformatics and biomedical informatics mainly in Europe and Canada due to European and National projects and research stays The area combines successfully four main fields of biomedical informatics namely health information engineering pattern recognition medical imaging and bioinformatics The Health Information Engineering area of IBIME has been working since 1999 in the field of the efficient use of informatio
8. The first time you open LinkEHR Ed you will see this window 5 LinkEHR Ed Integration Archetype Editor l Archetype Edit Reference Model Datasources Help La le ue a BHO i AY archetype Tree fy Iv Node Info E Console Select a New archetype or Open an existing one Capture 1 LinkEHR Ed first run LinkEHR Ed toolbar has available the most common used actions Capture 2 shows the meaning of buttons although they should be auto explicative enough New Archetype my Validation ADL View Open T e d sl Mapping View 2 to Line Help Add Archetype oN Find Replace Specialize Archetype p yp Saje in Export Integration Archetype Capture 2 The meaning of the buttons on the toolbar 2 Configure LinkEHR Ed User preferences can be changed in LinkEHR Ed s configuration dialog This dialog is located at Help gt Configure LinkEHR Ed The dialog has four tabs each one controlling a part of LinkEHR Ed see capture 3 a Languages tab controls the interface language of LinkEHR Ed Currently LinkEHR Ed is only available in English but we plan to release it on several languages That s why the buttons have no effect at this moment Visualization tab you can define the preferred visualization of the archetype tree in order to show the ontology description classes names or both and the default font for the archetype tree This also can be configured by pushing the button Ein the archetype tree vie
9. and XML according to the XML schema defined by the Consortium OpenEHR At its core lies the Archetype Object Model an object oriented model for archetypes this has also been adopted by CEN TC251 EN13606 It uses the Java implementation of the AOM and the ADL parser developed by ACode although several addition have been made in order to satisfy extra requirements such a multi reference model support and mapping to data sources With LinkEHR Ed new archetypes can be defined from scratch for instance to describe the data structure and semantics of legacy data such as messages or database schemas It is also possible to define new archetypes by specializing or altering existing ones such as those drawn from a public available archetype repository In any case LinkEHR Ed is intended to support the mapping to data sources NOTE LinkEHR Ed has two main uses As a multireference model editor of archetypes As an integration archetype editor which allows the integration and standardization of legacy data At this stage the first use is publicly available The second is not open sourced 5 Archetype Edition step by step tutorial This guide will show up the basis of LinkEHR Ed operation by showing you how to import both OpenEHR and CEN EN13606 reference models into LinkEHR Ed Later we will introduce how to open an archetype a creation of a new archetype and the specialization of an archetype 1 Running LinkEHR Ed for the first time
10. e the measurement by any means invasive or history history Structural node baseline reading baseline event in event history blood pressure internal systolic the peak systemic arterial blood pressure ov diastolic the minimum systemic arterial blood pressure we Capture 13 The ontology section form Console view This view shows the application messages and also has a tab to watch the path of the selected node of the definition tree E Console IParsing completed Ee Bo Dar Capture 14 The console view d ADL view Once an archetype has been loaded or created you can always switch to the ADL view in order to see and edit it Every change made in the ADL will be reparsed and validated before going back to the visual representation You can m e e switch to the ADL view by pushing the button and return to the previous view by pushing it again 17 openEHR EHR OBSERVATION blood pressure vl adl X i3definition 44 OBSERVATION art0000 matches 45 data matches 46 occurrences matches 0 1 matches events cardinality matches 1 unordered matches ft 48 EVENT at0006 occurrences matches 0 matches t 49 data matches 50 ITEM LIS5ST at0003 occurrences matches 0 1 matches items cardinality matches 0 ordered matches ELEMENT at0004 occurrences matches 0 1 matches value matches C DV QUANTITY lt property lt openebr 125 gt fiat Pray
11. e supported such as data types name spaces imports and includes reference models can be defined by using several files and a wide range of structures such as complex and simple types elements attributes inheritance by extension and restriction sequence choice all attributes patterns and groups and their respective facets e Domain types are not fully supported since they depend on particular reference model knowledge They are usually correctly parsed and edited in the ADL view but they are not shown visually e Access to terminology services is not yet implemented but terminology bindings can be defined e Only ADL 1 4 is supported e Uncontrolled errors can occur All notifications of bugs are welcome
12. e to open the import reference model wizard which is located under Reference Model Import Reference Model There you can introduce the organization name the model name and the XSD schemas defining the reference model as you can see in capture 4 Since we are constraining an OO model the distinction between classes and attributes is crucial In fact different types of constraints are applied accordingly For instance classes may be represented as elements or as type definitions In the former approach XML instances contain elements tagged with the class names while in the latter class names only appear in the schema When importing a new reference model it must be indicated whether or not classes are represented as elements in the schema It is supposes that all classes are represented in the same way In the case of the OpenEHR official XML Schemas you must set the combo Represent complex elements as to Complex types Import reference model Set an organization a name and the XML Schema files from where the new reference model will be created Organization name OpenEHR Reference model name EHR Represent complex elements as Complex types bal BaseTypes xsd Add XML Schema Composition xsd Content xsd Resource xsd Structure xsd Version xsd Delete Documentation file Capture 4 Importing OpenEHR reference model Once all this information has been introduced you can push Next button
13. etype constraint button of the toolbar 3 or by right clicking on the node of the tree where do you want to perform those actions captures 21 and 22 When you choose to include a new Complex Object a pop up will show up to choose which kind of object you want to add As shown in capture 23 you can choose the new node to be an object an internal reference to another object of the same type or an archetype slot You can delete a node objects and attributes selecting the Delete option from the right click menu over the corresponding node NOTE When two or more objects are assigned to a Single Attribute a virtual node called Alternatives will be created in the tree in order to show this specific fact It is only an informative node and has no other properties b gt LinkEHR Ed Integration Archetype Editor J C_Complex_Obj COMPOSITION Many ALLOWED Occurrences Min Max unbounded Ontology P arsing completed LAA arial Parsing completed Capture 22 and so does clicking with right button on a node 22 8 Type of specialization As Object As Archetype Internal Ref As Archetype Slot Capture 23 Choosing the type of the node Specializing an archetype To create a specialization archetype you only have to push the Specialize Archetype button of the toolbar or the menu Archetype gt Specialize A dialog will be displayed to select the parent archetype of the specia
14. lization and to introduce the specialization name Pushing Ok will create the specialization archetype with the structure of the parent archetype already included Then you can modify the specialized archetype the same way as told at step 7 Validating an archetype Once you have created an archetype from scratch or opened it from an available ADL file you can validate it by pushing the Validate button A This validation assures that the introduced constraints are effectively more constrained than those defined by a parent archetype if this is an specialization archetype or by the reference model In any other case an error message will be displayed with the path of the node where the validation failed 10 Save an archetype 23 Once you have finished the edition of an archetype you can save it trough the Save button or the Archetype gt Save menu You can choose an ADL format or an XML one just a prototype functionality in the second case 11 24 LinkEHR Ed current limitations LinkEHR Ed is a prototype tool from a research project in continuous evolution At this stage of the project it is not intended to be used in production or real environments but as a tool which gives a formal approach to the archetype edition process Some of its current limitations are e Some XML Schemas of other reference models can fail since their structure can be diverse Currently many of the characteristic of W3C XML schemas ar
15. n and communication technologies for the management of biomedical information Current lines of work are e Standardization and modelling of electronic clinical history by means of ontologies and archetypes of sanitary information e Semantic interoperability of health information systems e Integration of biomedical data e Modelling and management of phenotypic information e Visualization of biomedical information More info About LinkEHR Ed http pangea upv es linkehr About IBIME http www ibime upv es About ITACA http www itaca upv es About UPV http www upv es Contact Information You can contact us for any suggestions or bug notifications through the project web page see above or by sending an email to Jos Alberto Maldonado David Moner Diego Bosca jamaldo upv es damoca upv es diebosto upv es 2 About LinkEHR Ed LinkEHR Ed is an integration editor which allows mapping an archetype to existing data sources and generates the XQuery scripts that will extract and transform data from the sources into a standardized XML document It is a result of a research project funded by the Spanish Ministry of Education and Science reference TSI 2004 06475 C02 and TSI2007 66575 C02 3 LinkEHR Ed releases Previous versions LinkEHR Ed v0 1 Just an ADL editor LinkEHR Ed v0 5 Archetype editor independent of the underlying reference model used for defining attributes This is the open source version LinkEHR Ed v
16. ny time or directly jump to 1ts definition 4 Archetype Internal Reference Internal Reference Path Go source Capture 18 Internal reference view 19 e Archetype Slot Properties of an archetype slot includes and excludes can be edited from this form A Archetype Slot ARCHETYPE SLOT ANY ALLOWED Includes Excludes Indudes Capture 19 Archetype slot view e Primitive Object Each kind of primitive objects corresponding to the basic types string integer double boolean date time and datetime has its own form in order to define their constraints or assumed values O C String STRING CONSTRAINT C ANY ALLOWED Default O List a zA Z w_ 20 21 sas INTEGER CONSTRAINT LJ ANY ALLOWED Constraint Default O List OO et 2 Interval Set Min vy 2147483647 Set Max z 2147483647 Assumed Value Capture 20 Samples of String and Integer primitive objects views e Domain Types Since LinkEHR Ed is a model independent editor it is difficult to design an interface for editing particular domain types Due to this fact at this stage there is no visual interface for this kind of objects but they can still be edited textually by switching to the ADL view In order to edit the archetype you can add or delete new objects and attributes by clicking on the Add arch
17. ology Pu Pay Capture 10 The archetype tree containing all of its structure b Details view At the right side of the screen is where the different forms for introduction of data are loaded A different form 1s associated to each kind of node of the archetype tree see captures 11 12 and 13 openEHR EHR OBSERVATION blood pressure v1 Blood pressure All blood pressure measurements are recorded using this archetype There is a rich state model for use with exercise ECGs and Tilt Table measurements Not to be used for intravascular pressure Capture 11 The archetype header a description form All blood pressure measurements are recorded using this archetype Then Misuse Not to be used for intravascular pressure aa IEA Delete To record the systemic blood pressure of a person The measurement rec Capture 12 The language section form 16 ss ONTOLOGY E Term Definition Node Id atoo0o text description at 001 text description at 000 2 text description atvoo3 text description atooo4 text description at0005 text description at0o06 de Blutdruckmessung Die Messung des systemischen arteriellen Blu Historie Historie Basismessung Basismessung Blutdruck internal Men systolisch Der hOchste arterielle Blutdruck eines Zyklus diastolisch Der minimale systemische arterielle Blutdruck Paths C Blood pressur
18. own Choosing then an ADL file version 1 4 will load it into LinkEHR Ed If the ADL is not valid an error will be shown indicating the line where the error has been detected Moreover although the archetype tree can not be built the ADL code is available and can be accessed through Go to ADL button represented with this icon Looking at the ADL code will allow you to easily detect the error fix it and recompile the ADL text by pushing the button again to generate the visual representation of the archetype Editing an archetype The main window of LinkEHR Ed has four main components or views a Archetype tree view Here is where the archetype structure 1s represented as a tree including its header and description the definition tree the language section and the 15 ontology section capture 10 The button T switches the definition branch of the tree between technical and non technical view A Archetype Tree tip T E A openEHR EHR OBSERVATION blood pressure v1 E Definition E te Blood pressure 1 E data ELE history 0 1 SS events 1 5 ts 10 minute reading 0 1 E ts 5 minute reading 0 1 E any event 0 cts baseline reading 0 1 E ts Paradox 0 El Te Postural change 40 E protocol El E list structure 40 1 E items 0 5 E e Cuff size 0 1 H ts Instrument 0 1 H ts Location of measurement 0 1 gt ts Korotkoff sounds 0 1 Language Ont
19. s repositories Secondly we intend to employ archetypes for making public existing clinical information in the form of standardized EHR extracts For this purpose we take advantage of their data definition facet which was formalized in the previous section Archetypes explicitly specify the structure and content of valid instances of the underlying reference model to which interchangeable data instances must conform Thus it becomes necessary to transform data from the local sources with a particular structure or schema to meet the data structures defined by archetypes This problem is known in the literature as the data exchange translation or transformation problem Data exchange requires at the schema level an explicit representation of how the source and target schemas are related to each other these explicit representations are called mappings Mappings between two schemas can be specified in different ways They can be a query expressed in SQL or XQuery a predicate in first order logic a set of correspondences each of which relates a element from the source schema to an element from the target schema or even a third schema that relates the other two via two sets of correspondences 1 e a reified mapping At the data level data transformations operate on the instances of the schemas rather than on the schemas themselves they transform source instances into target instances according to the mapping defined between the corresponding schemas
20. w at any time during the archetype edition Paths tab you can change the paths used by LinkEHR Ed such as the internal physical repository path and the location of language and terminology XML files Default author tab you can insert the default information of the author in order to avoid retyping it everytime you create a new archetype The Default language refers to the primary language selected by default when creating a new archetype through the Create new archetype wizard Configure LinkEHR Ed Configure LinkEHR Ed Languages Visualization Paths Default Author Languages res Paths Default Author Interface language Prefered tree view EN A Only classes va Set active Font Import language Remove language Configure LinkEHR Ed Languages Visualization Pa Default Author Languages list path data LinkEHR terminology languages xml Terminologies list path data LinkEHR terminology terminologies xml Physical repository path Languages Visualization Paths Default Author Default Author Diego Bosc Tom s Organization ibime group Email diebosto upv es Remote repository URI none Map repository path 5 ES AR Spanish Argentina data nap ES B0 Spanish Bolivia ES CL Spanish Chile Default Language Capture 3 Configuration of linkEHR Ed 3 Adding the OpenEHR reference model to LinkEHR Ed To import a new reference model you hav
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