CTS2-LE Building Blocks - Versionsgeschichte

Billig am 18. Januar 2022 um 16:55 Uhr

2022-01-18T16:55:47Z

Billig: /* Terminology Editing and Processing */

2020-09-04T12:02:03Z

‎Terminology Editing and Processing

Billig: to be updated ->Ben

2016-08-24T20:02:04Z

to be updated ->Ben

Krebs: /* Terminology Editing and Processing */

2015-09-29T09:43:38Z

‎Terminology Editing and Processing

Billig am 15. Juli 2015 um 11:26 Uhr

2015-07-15T11:26:05Z

Billig am 15. Juli 2015 um 11:24 Uhr

2015-07-15T11:24:33Z

Billig am 9. Juli 2015 um 15:01 Uhr

2015-07-09T15:01:14Z

Caumanns: /* Full Text Classificator */

2015-06-16T14:09:14Z

‎Full Text Classificator

Caumanns: /* CTS2-LE Navigator */

2015-06-16T12:47:18Z

‎CTS2-LE Navigator

Caumanns: /* CTS2-LE Navigator */

2015-06-05T08:41:00Z

‎CTS2-LE Navigator

@@ Zeile 1: / Zeile 1: @@
 == CTS2-LE Layered Architecture ==
-[[Datei:CTS2-LE Layers.png|320px|right]] CTS2-LE Terminology Server utilizes semantic technologies for representing, providing and processing CTS2 artefacts. The main benefits of this approach are
+[[Datei:CTS2-LE Layers.png|320px|right]] CTS2-LE Terminology Server utilizes semantic technologies for representing, providing and processing artefacts. The main benefits of this approach are
 * the conceptual nearness to the nature of the artefacts to store, namely controlled vocabularies and its derivate artefacts,
 * semantic processing and querying in a direct way, and
 * to be able to manage a huge amount of linked medical data.
-Concretely, CTS2-LE store is based on the Jena Framework  plus additional components for searching and constraining the RDF base. The system components and its functionality are explained bottom to top with the help of the overall system architecture shown in the figure to the rigth. The persistence layer is split into two storage systems, namely a full text index for performant search (Lucene) and the RDF (quad )store (Jena-TDB) for holding all CTS2 artefacts as RDF graphs. As the system backbone the Jena Framework is used, which offers rich functionality to process and maintain the RDF graphs on a basic level.
+Concretely, the store is based on the Jena Framework  plus additional components for searching and constraining the RDF base. The system components and its functionality are explained bottom to top with the help of the overall system architecture shown in the figure to the rigth. The persistence layer is split into two storage systems, namely a full text index for performant search (Lucene) and the RDF (quad )store (Jena-TDB) for holding all artefacts as RDF graphs. As the system backbone the Jena Framework is used, which offers rich functionality to process and maintain the RDF graphs on a basic level.
 The Jena Framework is enhanced by some components in order to comfortably handle the (possible huge amount of) artefacts. CTS2-LE
 * explicitly partitions the whole RDF graph by means of the so-called named graphs feature,
 * contains a lightweight SPARQL template mechanism and engine, and
-* introduces a schema language for RDF graphs together with a validation component in order to ensure that all data is valid with respect to the CTS2 information model.
+* introduces a schema language for RDF graphs together with a validation component in order to ensure that all data is valid with respect to the FHIR/CTS2 information model.
-[[Datei:Sparql and rdf.png|200px|right]]The tier above Jena (CTS2-LE-BL) contains all CTS2-specific functionality and mainly uses SPARQL-Templates. At this tier customized vocabulary loaders are located which, for instance, transform ClaML-defined vocabularies such as ICD and OPS to RDF structures. Web-CTS2-LE is the component for handling REST calls aligned to the FHIR specification. CTS2-LE provides an so-called CTS2-Navigator to browse and search vocabularies as well as retrieving similar concepts based on the vector space model of Lucene.
+[[Datei:Sparql and rdf.png|200px|right]]The tier above Jena (CTS2-LE-BL) contains all specific functionality and mainly uses SPARQL-Templates. At this tier customized vocabulary loaders are located which, for instance, transform ClaML-defined vocabularies such as ICD and OPS to RDF structures. Web-CTS2-LE is the component for handling REST calls aligned to the FHIR specification. CTS2-LE provides an so-called Navigator to browse and search vocabularies as well as retrieving similar concepts based on the vector space model of Lucene.
 The figure to the right shows some essential components. At the bottom the RDF graph is partitioned such that every vocabulary is represented by a named graph for better handling the exchange of vocabularies as a whole. Above that tier the main work is done by the Jena SPARQL engine for accessing and processing vocabularies and its corresponding artefacts such as value sets and mappings.
-So-called RDF signatures are used to define a constraining RDF schema according to the CTS2 information model.  Moreover, this F-Logic oriented RDF schema definition for CTS2 is helpful in formulating SPARQL queries, since it directly reflects the RDF graph structure. Validating store content according to these schemata is mainly done by means of the SPARQL engine. Furthermore, lightweight SPARQL templates can be defined to support reuse of queries by parameterization.
+So-called RDF signatures are used to define a constraining RDF schema according to the FHIR/CTS2 information model.  Moreover, this F-Logic oriented RDF schema definition is helpful in formulating SPARQL queries, since it directly reflects the RDF graph structure. Validating store content according to these schemata is mainly done by means of the SPARQL engine. Furthermore, lightweight SPARQL templates can be defined to support reuse of queries by parameterization.
-== Terminology Editing and Processing ==
+As sketched above, CTS2-LE manages all terminology artifacts as FHIR/CTS2-compliant RDF graphs using a RDF (quad )store. By wrapping these data managing component with a powerful SPARQL engine, a generic and standards-based interface is provided that allows to place enhanced semantic data access and processing services on top of the core data managing engine. A complementary Lucene index is is utilized for gaining outstanding search performance.
 <!--

@@ Zeile 21: / Zeile 21: @@
 As sketched above, CTS2-LE manages all terminology artifacts as CTS2-compliant RDF graphs using a RDF (quad )store. By wrapping these data managing component with a powerful SPARQL engine, a generic and standards-based interface is provided that allows to place enhanced semantic data access and processing services on top of the core data managing engine. A complementary Lucene index is is utilized for gaining outstanding search performance.
 This section introduces the set of services already provided as part of the standard CTS2-LE distribution.
@@ Zeile 33: / Zeile 34: @@
 [[Datei:Navigator screenshot 1.jpg|360px|right]]The CTS2-LE Navigator provides a graphical user interface for searching and browsing terminologies. It provides interactive means for:
-<!--
+<  !--
 * [[CTS2-LE Navigator: Managing Terminologies|Managing the lifecycle of terminologies and value sets]] (loading, deleting, updating and versioning)
--->
+--  >
 * [[CTS2-LE Navigator: Browsing through Terminologies|Browsing through terminologies]]
 * [[CTS2-LE Navigator: Searching for Concepts and Terms|Searching for concepts and terms]] (within single terminologies or even across multiple terminologies)
 * [[CTS2-LE Navigator: Searching for Similar Concepts|Searching for Similar Concepts]]
 * [[CTS2-LE Navigator: Resolving and Displaying Value Sets|Resolving and displaying value sets]]
-<!--
+<  !--
 * [[CTS2-LE Navigator: Semantic Full Text Classification|Semantic full text classification]]
--->
+--  >
 === Terminology Loaders ===
 Besides the FHIR import interface described [[CTS2-LE REST API: Update Value Set|here]], there are specific Loaders that can be used to integrate common terminologies. For further information please visit [[CTS2-LE Loading Core Terminologies]].
-<!--
+<  !--
 == Third Party Tools ==
 Due to its open, standards-based interfaces CTS2-LE is perfectly suited for thrid-party tools to connect to CTS2-LE for providing added-value functionalities on top of CTS2 terminology artifacts.
@@ Zeile 55: / Zeile 56: @@
 The CTS2-LE Freeplane Plugin is an Add-On to Freeplane which enables terminology editors to interactively define and edit terminologies and value sets as mind maps. The Add-On is seamlessly integrated with the Freeplane GUI and workflow. By connecting to a CTS2-LE server from within the freeplane modelling GUI, the Add-On can e.g. fetch candidate concepts for a value set from given text phrases (e.g. if one adds a node named "birk poll allergy" to a freeplane mind map in value set editing mode, the Add-On automatically fetches information about all concepts from CTS2-LE which may be suitable for representing that node. By selecting one of these candidate concepts, the freeplane node gets linked to that concept which semantically corresponds to adding the concept to the value set under construction). Newly created or modified termnologies and value sets can either be uploaded to a CTS2-LE server directly out of freeplane or saved to the filesystem in FHIR value set format.
--->
+--  >
-<!--
+<  !--
 For further information see the online documentation about:
 * [[Freeplane CTS2-LE Plugin: Installation|Installation and Configuration of the CTS2-LE Freeeplane Plug-In]]
 * [[Freeplane CTS2-LE Plugin: Editing Terminologies|Editing Terminologies using the CTS2-LE Freeeplane Plug-In]]
 * [[Freeplane CTS2-LE Plugin: Editing Value Sets|Editing Value Sets using the CTS2-LE Freeeplane Plug-In]]
 -->

@@ Zeile 47: / Zeile 47: @@
 Besides the FHIR import interface described [[CTS2-LE REST API: Update Value Set|here]], there are specific Loaders that can be used to integrate common terminologies. For further information please visit [[CTS2-LE Loading Core Terminologies]].
 == Third Party Tools ==
 Due to its open, standards-based interfaces CTS2-LE is perfectly suited for thrid-party tools to connect to CTS2-LE for providing added-value functionalities on top of CTS2 terminology artifacts.
 === CTS2-LE Freeplane Plug-In ===
-[[Datei:Freeplane screenshot 1.png|right|300px]]Freeplane is an open source mind mapping and knowledge management software (-->[http://www.freeplane.org/wiki/index.php/Main_Page Freeplane Homepage]). Freeplane provides a powerful graphical user interface for editing and classifying mind maps in a very intuitive manner. The software provides a powerful mechanism to extend the core functionality through Add-Ons and scripting.
+[[Datei:Freeplane screenshot 1.png|right|300px]]Freeplane is an open source mind mapping and knowledge management software ([http://www.freeplane.org/wiki/index.php/Main_Page Freeplane Homepage]). Freeplane provides a powerful graphical user interface for editing and classifying mind maps in a very intuitive manner. The software provides a powerful mechanism to extend the core functionality through Add-Ons and scripting.
 The CTS2-LE Freeplane Plugin is an Add-On to Freeplane which enables terminology editors to interactively define and edit terminologies and value sets as mind maps. The Add-On is seamlessly integrated with the Freeplane GUI and workflow. By connecting to a CTS2-LE server from within the freeplane modelling GUI, the Add-On can e.g. fetch candidate concepts for a value set from given text phrases (e.g. if one adds a node named "birk poll allergy" to a freeplane mind map in value set editing mode, the Add-On automatically fetches information about all concepts from CTS2-LE which may be suitable for representing that node. By selecting one of these candidate concepts, the freeplane node gets linked to that concept which semantically corresponds to adding the concept to the value set under construction). Newly created or modified termnologies and value sets can either be uploaded to a CTS2-LE server directly out of freeplane or saved to the filesystem in FHIR value set format.
+-->
 For further information see the online documentation about:
 * [[Freeplane CTS2-LE Plugin: Installation|Installation and Configuration of the CTS2-LE Freeeplane Plug-In]]
 * [[Freeplane CTS2-LE Plugin: Editing Terminologies|Editing Terminologies using the CTS2-LE Freeeplane Plug-In]]
 * [[Freeplane CTS2-LE Plugin: Editing Value Sets|Editing Value Sets using the CTS2-LE Freeeplane Plug-In]]

@@ Zeile 45: / Zeile 45: @@
 === Terminology Loaders ===
-: ''(--> Franziska)''
+Besides the FHIR import interface described [[CTS2-LE REST API: Update Value Set|here]], there are specific Loaders that can be used to integrate common terminologies. For further information please visit [[CTS2-LE Loading Core Terminologies]].
 == Third Party Tools ==

@@ Zeile 33: / Zeile 33: @@
 [[Datei:Navigator screenshot 1.jpg|360px|right]]The CTS2-LE Navigator provides a graphical user interface for searching and browsing terminologies. It provides interactive means for:
-<-!!
+<!--
 * [[CTS2-LE Navigator: Managing Terminologies|Managing the lifecycle of terminologies and value sets]] (loading, deleting, updating and versioning)
 -->

@@ Zeile 1: / Zeile 1: @@
 == CTS2-LE Layered Architecture ==
-[[Datei:CTS2-LE Layers.png|320px|right]] CTS2-LE CTS2 Terminology Server utilizes semantic technologies for representing, providing and processing CTS2 artefacts. The main benefits of this approach are
+[[Datei:CTS2-LE Layers.png|320px|right]] CTS2-LE Terminology Server utilizes semantic technologies for representing, providing and processing CTS2 artefacts. The main benefits of this approach are
 * the conceptual nearness to the nature of the artefacts to store, namely controlled vocabularies and its derivate artefacts,
 * semantic processing and querying in a direct way, and
@@ Zeile 12: / Zeile 12: @@
-[[Datei:Sparql and rdf.png|200px|right]]The tier above Jena (WebCts2-Le) contains all CTS2-specific functionality and mainly uses SPARQL-Templates. At this tier customized vocabulary loaders are located which, for instance, transform ClaML-defined vocabularies such as ICD and OPS to RDF structures. CTS2-WS (Web-Service) is the component for handling REST calls defined in the CTS2 specification. The topmost tier contains the clients for CTS2 access. Besides web service clients CTS2-LE provides an so-called CTS2-Navigator to browse and search vocabularies as well as retrieving similar concepts based on the vector space model of Lucene.
+[[Datei:Sparql and rdf.png|200px|right]]The tier above Jena (CTS2-LE-BL) contains all CTS2-specific functionality and mainly uses SPARQL-Templates. At this tier customized vocabulary loaders are located which, for instance, transform ClaML-defined vocabularies such as ICD and OPS to RDF structures. Web-CTS2-LE is the component for handling REST calls aligned to the FHIR specification. CTS2-LE provides an so-called CTS2-Navigator to browse and search vocabularies as well as retrieving similar concepts based on the vector space model of Lucene.
 The figure to the right shows some essential components. At the bottom the RDF graph is partitioned such that every vocabulary is represented by a named graph for better handling the exchange of vocabularies as a whole. Above that tier the main work is done by the Jena SPARQL engine for accessing and processing vocabularies and its corresponding artefacts such as value sets and mappings.
@@ Zeile 19: / Zeile 19: @@
 == Terminology Editing and Processing ==
-As sketched above, CTS2-LE manages all terminology artifacts as CTS2-compliant RDF graphs using a complementary Lucene vector space for gaining outstanding search performance. By wrapping these data managing components with a powerful SPARQL engine, a generic and standards-based interface is provided that allows to place enhanced semantic data access and processing services on top of the core data managing engine. This section introduces the set of services already provided as part of the standard CTS2-LE distribution.
+As sketched above, CTS2-LE manages all terminology artifacts as CTS2-compliant RDF graphs using a RDF (quad )store. By wrapping these data managing component with a powerful SPARQL engine, a generic and standards-based interface is provided that allows to place enhanced semantic data access and processing services on top of the core data managing engine. A complementary Lucene index is is utilized for gaining outstanding search performance.
 === CTS2-LE REST API ===
-CTS2-LE implements a REST interfaces to provide terminology consuming applications easy access the most common subset of services as defined in the CTS2 Service Functional Model. The API recently consists of terminology access and processing services for:
+The API recently consists of terminology access and processing services for:
 * resolve and/or fetch an FHIR origined value set (or terminology) which is identified by it's URI ([[CTS2-LE REST API: Resolve Value Set|ResolveValueSet]]). This API can e.g. be used for populating web forms with value set contents at run time.
 * fetching the details of a concept which is identified through a codesystem and code ([[CTS2-LE REST API: Requesting Concept Details|RequestConceptDetails]]). This API can e.g. be used for obtaining the full description of a coded value within a CDA document.

@@ Zeile 29: / Zeile 29: @@
 === CTS2-LE Navigator ===
-{|
-|-
+[[Datei:Navigator screenshot 1.jpg|360px|right]]The CTS2-LE Navigator provides a graphical user interface for searching and browsing terminologies. It provides interactive means for:
 * [[CTS2-LE Navigator: Managing Terminologies|Managing the lifecycle of terminologies]] (loading, deleting, updating and versioning)
 * [[CTS2-LE Navigator: Managing Value Sets|Managing the lifecycle of value sets]] (loading, deleting, updating and versioning)
@@ Zeile 39: / Zeile 38: @@
 * [[CTS2-LE Navigator: Resolving and Displaying Value Sets|Resolving and displaying value sets]]
 * [[CTS2-LE Navigator: Semantic Full Text Classification|Semantic full text classification]]
 === Terminology Loaders ===