CTS2 Linked Data Edition Terminology Server
Controlled vocabularies (also known as code systems or terminologies) are common information artefacts in healthcare. They allow for univocally and precisely referencing of concepts and are core foundation of any semantic processing of health data. In particular all electronic communication in healthcare relies on coded concepts for semantic interoperability and automated data processing.
The Object Management Group's Common Terminology Services Version 2 (CTS2) standard defines an accepted industry standard service interface to share, query and maintain value sets and other terminology artifacts. The CTS2 specification is structured within a platform independent model that provides two profiles:
- Structural profiles define how code systems, associations, or value sets are organized;
- Functional profiles define fundamental operations of persistent storage (CRUD) in an information system that change these structures.
One method to achieve compliance with the structural profiles of CTS2 is to use semantic web technologies that are widely used for vocabularies. In this way, CTS2 artifacts such as code systems, code system elements (i.e., codes and their designations), associations and value sets (i.e., sets of code system elements) can be processed with reasoning engines including code member validations.
The CTS2 Linked Data Edition (CTS2-LE) terminology server provided by Fraunhofer FOKUS follows that foundation. It relies on the the Resource Description Framework (RDF) in conjunction with a RDFS-based schema vocabulary oriented towards the Frame Logic. So-called RDF signatures, based on this schema vocabulary, describe structural constraints according to the CTS2 information model. Likewise, arbitrary object graphs can be processed and stored with these RDF signatures.
Inhaltsverzeichnis
CTS2-LE Overview
This section provides an overview about CTS2-LE. It introduces the CTS2-LE building blocks and summarizes the most important functional features provided by CTS2-LE.
- CTS2-LE Fact Sheet (German)
- The CTS2-LE Fact Sheet provides an overview of CTS2-LE considering the implemented CTS2 functionalities and additional usability related features.
- CTS2-LE Building Blocks
- The foundation of CTS2-LE features a structural compliance to the OMG CTS2 Information Model, is linked-data ready by the means of W3C RDF, and is accessible through a HL7 FHIR and REST API as well as supporting the definition, composition and import of value sets. The knowledge base functionality is implemented with RDF as the representation language providing linkage capabilities for intra- or cross-domain artifacts such as HL7 CDA and HL7 FHIR. This section describes the architecture and internal design of CTS2-LE.
- CTS2-LE Supported Terminologies
- CTS2-LE is highly suitable for representing netlike vocabularies of varying complexity. Thus, it facilitates the integration of several healthcare relevant terminologies. This section gives an overview of the vocabularies that can be loaded so far.
- CTS2-LE Interoperability
- CTS2-LE is build upon international standards and provides multiple standard interfaces for connecting to external services. This section gives an overview on the standards supported by CTS2-LE and how these can be utilized for integrating CTS2-LE with third party products.
- Further Information Sources for CTS2-LE
- Fraunhofer FOKUS has published various papers and brochures about CTS2-LE in particular and terminology services in general. This section provides links to online resources related to CTS2 and CTS2-LE.
- Licence and Availability Notes
- When distributing CTS2-LE along with its supported terminologies, licence restrictions have to be considered. This section outlines the terminology specific terms of distribution.
CTS2-LE Installation, Deployment, and Setup
This section covers the installation and initial setup of CTS-LE within an organization.
- Prerequisites
- This section describes the hardware, OS and network requirements for installing CTS2-LE as a stand-alone-system on a server.
- Installation, Deployment, and Setup V2
- CTS2-LE is provided as a set of libraries and executables for the various system building blocks. This section describes how to deploy, configure and activate these components for specific usage scenarios.
- Installation, Deployment, and Setup V3
- V3 is designed to run in distributed mode, i.e. search engine (solr), database (fuseki quad store), and service layer can run separately. Furthermore, terminologies can be loaded remotely.
- Security Configuration
- CTS2-LE standard configuration allows unrestricted read access while administrative functionalities (e. g. loading/updating terminologies) is restricted to registered named users. This section describes how to configure these defaut security settings and how enhanced security services (e. g. full access control) may be linked with CTS2-LE.
The CTS2-LE Navigator provides a graphical user interface for online browsing. This sections describes the functionalites of the CTS2-LE Navigator and how to use these.
- Browsing through Terminologies
- This section describes how CTS2-LE Navigator can be used for browsing through hierarchal and networked termonologies.
- Searching for Concepts and Terms
- CTS2-LE allows to search for concepts and terms either with a single or within multiple terminologies. This section describes how CTS2-LE Navigator's search features can be used and configured.
- Searching for Similar Concepts
- Whenever a concept is selected in CTS2-LE, the Navigator can be triggered to perform a full-text search across the full terminology base to discover concepts which are similar to the selected concept. This feature can e.g. used to ease the manual definition of mappings across terminologies. This section describes how such enhanced search features can be used and configured within CTS2-LE Navigator.
- Resolving and Displaying Value Sets
- CTS2 compliant value sets are defined as sets of references into terminologies. This section describes how such reference sets can be resolved into concept lists and how such lists can be displayed and exported in a standard format.
CTS2-LE Web Services
CTS2-LE provides a simple REST interface for integrating CTS2-LE terminology services with custom and third-party applications. This section provides the technical specification of the CTS2-LE REST Application Programming Interface including sample code snippets for each interface.
FHIR R4
CTS2-LE supports essential parts of the FHIR REST API that will deprecate most of the API below. Not all parameters are supported, but in the context of customization for a project it will be enhanced. The following operations are supported:
General
- read
- update
- if extra parameter ext:deactivateExistent == true then the existing resource is not deleted, only deactivated. It is recommended for huge stores/indexes due to high costs of updates in quad stores.
- delete
Code Systems
- lookup
- supported parameters: code, system, version, coding, displayLanguage
- validate-code
- supported parameters: url, code, version, display, coding, codeableConcept, displayLanguage
- subsumes
- supported parameters: codeA, codeB, system, version, codingA, codingB
Value Sets
- expand
- supported parameters: url, valueSetVersion, includeDesignations
- validate-code
- supported parameters: url, valueSetVersion, code, system, systemVersion, display, coding, codeableConcept, displayLanguage
FHIR-based (deprecated)
- Read Code System
- reads a code system.
- Resolve Value Set (multi-modal)
- provides means to resolve and/or fetch an FHIR origined value set (or code system).
- Resolve Complete Value Set
- provides means to resolve and/or fetch an FHIR origined value set (or code system) which is identified by it's URI.
- Request Concept Details
- used for fetching the details of a concept which is identified through a codesystem and code.
- Check Value Set Containment
- allows to check wether a code (from a code system) is contained in a Value Set.
- Update Value Set / Code System
- allows to create or update a FHIR coded value set (or code system).
- Delete Value Set / Code System
- allows to delete a FHIR coded value set (or code system).
SPARQL
- SPARQL Query
- Due to the full RDF-encoding of all terminology artifacts, CTS2-LE allows for arbitrary queries within and across terminologies, value sets, concepts, and concept relationships. This API provides means to transmit a standard SPARQL query to CTS2-LE. The query result is provided in standard SPARQL Query Results XML Format.
CTS2 REST-API (deprecated in future)
Most of the API below is supported by the FHIR R4 API. FHIR is emerging as a modern standard to cover all aspects of interoperable communication between all agents (human or machine) in eHealth.
The below services mainly implement the standard services as specified in the documents provided by OMG/HL7. For further references (to the normative documents or XML schema files) please visit this site. Please note that these services are not fully tested at this time. Hence, they are not available on any machine.
- Read Code Systems and Code System Versions
- Read Entity Descriptions
- Read Maps and Map Versions
- Read Value Set Definitions
Sharing Value Sets (SVS)
Classification Markup Language (ClaML)
Futher Services
- Concept Suggestion
- retrieve results from suggestion (plain, restricted)
- Concept Search
- perform search operations (plain, restricted, similar)
- EXCEL/CSV Value Set Catalog Import
CTS2-LE Terminology Loading
Loading terminologies and value sets is achieved by applying one of the following modes:
- an online mode which allows to integrate resources into a running CTS2-LE server instance and
- an offline mode which integrates resources into a shut down CTS2-LE server instance.
Choosing one of these options is not arbitrary but dependent on the provided format. In order to load terminologies on the fly, they have to be structured according to the FHIR value set definition. These files can then be integrated by means of the CTS2-LE REST-API, For any other representation of a terminology, a specific loader has to be prepared.
- CTS2-LE Loading Core Terminologies
- CTS2-LE provides standard interfaces for importing terminologies and value sets. While some terminologies are distributed in such standard formats , many widely used terminologies are only available in a proprietary format and therefore need specific loaders that map this proprietary format onto the CTS2 data model. This section lists all terminologies which are recently supported by CTS2-LE together with information on how to obtain and import each terminology.
- CTS2-LE FHIR Loader
- HL7 FHIR provides a standard format for encoding value sets and terminologies. The CTS2-LE FHIR Loader allows to upload terminology resources to CTS2-LE using the standard FHIR value set resource definiton. In order to integrate a value set or terminology the usage of our FHIR REST API is recommended.
CTS2-LE can be used to manage and provide any kind of flat, hierarchical, poly-hierarchical or even networked terminology. To ease the integration of widely used terminologies into CTS2-LE Fraunhofer FOKUS provides various loaders for dedicated terminologies. These loaders always perform a mapping onto the CTS2 information model. The following links provide information on the general approach as well as on decicated mappings of certain terminologies.
- Mapping Terminologies to CTS2-LE
- This section describes the general approach for mapping a standard terminology to CTS2-LE.
- Proprietary CTS2-LE Terminology Loaders
- Please see the list below for links to descriptions of CTS2-LE loaders for terminologies which are not available in FHIR format. The description of each loader includes information on the loader's input and output format together with a description on how to use the loader to import a terminology into CTS2-LE.
- Systematized Nomenclature of Human and Veterinary Medicine - Clinical Terms (SNOMED-CT)
- Logical Observation Identifiers Names and Codes (LOINC)
- Medical Subject Headings (MeSH)
- Alpha-ID
- Anatomical Therapeutic Chemical Classification (ATC) Defined Daily Dose (DDD) und Darreichungsformen
- International Statistical Classification of Diseases and Related Health Problems Revision 10 (ICD-10)
- Operationen- und Prozedurenschlüssel (OPS)
- Unified Code for Units of Measure (UCUM)
- Klassifikation therapeutischer Leistungen in der medizinischen Rehabilitation (KTL)
CTS2-LE Solution Management
- CTS2-LE Licensing
- CTS2-LE is distributed by Fraunhofer FOKUS under a commercial license. This section provides information about the licensing terms and conditions for various CTS2-LE usage scenarios.
- CTS2-LE Release Management
- Fraunhofer FOKUS is continuosly maintaining and further developing CTS2-LE. This section gives insight into the CTS2-LE development roadmap by sketching CTS2-LE add-ons and improvements which are under development at Fraunhofer FOKUS.
- CTS2-LE Wish List
- You have an idea for a cool new feature for CTS2-LE? There is some interface you desperately need for your terminology consuming solution? You have discovered a useful terminology that should be distributed through the public CTS2-LE? The CTS2-LE Wish List summarizes all ideas for new CTS2-LE featurs and acts as a major input to the CTS2-LE development roadmap.
