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The sections on this page provide an overview of the current implementations that demonstrate CTS2 REST examples. These examples demonstrate browsing, searching, forms completion, mapping and incremental versioning and updates. We also have a video presentation of these implementations.

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Project Goals

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 here

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and a list of the translated Ajax Widgets can be found here

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Results

As expected, a number of issues were encountered in this process including:

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• States how content and structure of a terminological resource maps to the CTS2 information model
  
  • Could be for import/export
  • Could also apply to backing store
• Identifies terminology specific business rules that services must enforce
• Aligns CTS2 w/ organization workflow
• Identifies any extensions to CTS2 specific to the given terminology

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