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CTS2 In Action Video

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Kevin Peterson
February 2012
Demonstration of various applications using CTS2 services.

CTS2 Over BioPortal Video

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Kevin Peterson
January 2012
Demonstration of a CTS2 compliant wrapper built over NCBO's BioPortal.

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The NCBO BioPortal

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was created "to access and share ontologies that are actively used in biomedical communities." To meet this goal, BioPortal has developed the BioPortal REST API
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, which can be used to access BioPortal using http. One of the primary applications of this API are web browsers that can use Ajax widgets to browse and access ontology content for a variety of uses. Samples of some of these widgets can be found here.

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We began by gathering a list of the key BioPortal resources - Ontology, AbstractConcept, Class, Property and Instance along with various lists. Lacking a formal XML Schema for these resources, we used a combination of sample content from the REST service and the java bean classes for each of the resources to assemble lists of the properties for each of these resources, their types and, where it could be determined their cardinality. We went through these lists, gathering sample input from the REST API - both in form of lists of elements and individual elements. We soon discovered that the content of a resource that appeared in list of resources (e.g. ontologies

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and an individual resource instance bpr:ontologies/39002
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were not the same. Some attributes appeared in both places, some just in the resource instance and some did not appear at all.

We took these lists and created a first shot at the CTS2 equivalents - the results of which can be found in Bioportal ontologies on the Mayo informatics service

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for the ontology resource and BioPortal terms on the Mayo informatics service
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for the "terms" (aka. Concept). There were a number of conceptual issues that were uncovered in this process, including:

  • CTS2 has a notions of Code System and Code System Version. While BioPortal has similar concepts - "virtual ontology" and "ontology" in the ontology interface and "ontology" and "ontology version" in the search interface, the "virtual ontology" has no attributes besides its identifier.
  • BioPortal treats both full ontologies and subsets derived from full ontologies as instances of "ontology". Lists and queries apply to both types of resource -
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    - a list of the latest version of ontologies on bioontology.org
    returns both the ontologies themselves as well as all subsets. Similarly, term queries return both the ontology in which the term is defined and any subsets that include that term. CTS2 treats Code Systems (ontologies) and Value Sets (subsets) as separate resources. Lists and queries go against one or the other resource but not both.
  • BioPortal assumes that all terms are instances of exactly one of "class", "property" or "instance". CTS2 allows entity (the equivalent of "term") to exist without making this distinction. In addition, while the CTS2 REST model does not clearly show how this could be done, the intent of the CTS2 model is to allow an entity to simultaneously be a Class and Instance, Class and Property, etc.

We then created a map

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from each of the BioPortal REST signatures
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and the equivalent CTS2 REST signature(s)
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, wherever possible.

These documents were then used to construct a CTS2 REST Server that used the BioPortal REST services as the back end implementation. In addition, we took a number of the interesting BioPortal Ajax widgets and modified them to use the CTS2 REST api instead. A synopsis of the REST services that were implemented can be found on the BioPortal Wrapper Summary page

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and a list of the translated Ajax Widgets can be found on the BioPortal Ajax page
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  • Specify how the HL7 MIF syntax and semantics map to the CTS2 Model, optionally identifying any HL7 specific extensions
  • Specify how the HL7 terminology related business rules and workflow would be represented in CTS2 Service Implementations.

Target Dates:

Task

Target Date

Project Team Inception

2011 December

Complete Draft Implementation Guide

2012 March

Submit for DSTU Ballot

2012 May Ballot

Consider Comments from the DSTU Ballot

2012 June

Submit to TSC for DSTU Approval

2012 July

Close Project (project end date)

2012 September WGM

Project Wiki and Documentation can be found at HL7 Wiki - CTS2 Implementation Guide Project

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Various NCBO Bioportal Widgets have be adapted for use with a CTS2 compliant service, available on the Mayo informatics service

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A terminology mapping browser that allows users to search and browse mappings from SNOMEDCT to ICD10

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A tool to search for text-based matches of vocabulary content

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  • Autocomplete ontology selection
  • Search based on a single terminology or all terminologies
  • Search results shown in summary and detailed view
  • Logging console panel to show actual REST queries being sent to the CTS2 service

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