NCI Thesaurus The NCIt is a reference biomedical ontology used by the NCI and a growing number of other systems.12 ‘NCIt covers vocab- ulary for clinical care, translational and basic research, and public information and administrative activities. The content is focused on cancer, but contains an increasing amount of terminology that is not speciﬁc to cancer as the number of non- cancer users and partners increases. NCIt is a concept-based terminology, with more than 70 000 concepts hierarchically organized in 19 distinct domains. It provides terminological informationddeﬁnitions, synonyms, and other concept proper- ties. The NCIt is the main source used for annotating the data elements in the caDSR; further NCIt entries reference corresponding nodes in the UMLS SN.’9 12 UMLS semantic network and groups ‘The UMLS SN provides information about the set of basic semantic types, or categories, which may be assigned to NCIt concepts; it also deﬁnes the set of relationships that may hold between semantic types.’9 13 ‘The SN contains 133 semantic types and 54 relationships. The SN serves as an authority for the semantic types that are assigned to concepts in the Meta- thesaurus. The SN deﬁnes these types, both with textual descriptions and by means of the information inherent in its hierarchies. There are major groupings of semantic types for organisms, anatomical structures, biologic function, chemicals, events, physical objects, and concepts or ideas.’9 14 15 Semantic web technologies The world wide web consortium (W3C) is the main standards body for the world wide web. The goal of the W3C is to develop interoperable technologies and tools as well as speciﬁcations and guidelines to lead the web to its full potential. W3C recom- mendations have several maturity levels: working draft, candi- date recommendation, proposed recommendation, and W3C recommendation. The resource description framework (RDF),16 web ontology language (OWL),17 and SPARQL18 speciﬁcations have all achieved the level of W3C recommendations, and are becoming generally accepted and widely used. OWL is a stan- dard ontology language for the semantic web, and is used for ontology modeling by building hierarchies of classes describing concepts in a domain and relating the classes to each other using properties. RDF is a model of directed, labeled graphs that is used to represent information in the web.16 SPARQL is a query language for RDF graphs. SPARQL queries are expressed as constraints on graphs, and return RDF graphs or sets as results. A ‘triple store’ is a database for the storage and retrieval of RDF meta-data, ideally through standard SPARQL query language. Some triple stores can store billions of triples. In addition, the XML Semantics Reuse methodology is a typical semantic web technology, which focuses on moving meta-data from the XML domain to the semantic web.19 MATERIALS AND METHODS We examined three resourcesdthe caDSR CDEs, the NCIt and the UMLS semantic types and groups. Figure 1 shows the linkage between the data element, value domain, enumerated value domain, permissible values, NCIt-based concept annotations, and UMLS semantic types and groups, as well as a typical example of each element. Note that the value meaning of ‘No (C49487)’ is coupled with a different semantic type than ‘Yes (C49488)’. Although these still fall within the same semantic group ‘CONC’, and would not be caught by this study, this juxtapo- sition is still curious and should probably be examined further. J Am Med Inform Assoc 2012;19:e129ee136. doi:10.1136/amiajnl-2011-000739 Research and applications Materials First, we accessed the caDSR CDE browser11 and downloaded all non-retired production CDEs (ie, the CDEs that do not have Workﬂow status ¼ RETIRED) as of April 14, 2011. These CDEs were rendered in XML format. Second, we downloaded the latest version 11.04d of NCIt from the NCI EVS Downloads website.20 We used a copy of the inferred OWL ﬁle that contains the terminology from the NCIt that includes both stated and inferred relationships and excludes retired concepts. Note that excluding the retired concepts may affect currently generated result sets, as the terminological annotations asserted in the caDSR may be based on an old version of NCIt (see the Discussion section). Third, we downloaded a copy of the UMLS semantic groups ﬁle that provides the mappings between 15 semantic groups and 133 semantic types.13 Methods Figure 2 shows the system architecture of the semantic web infrastructure implemented for quality evaluation of CDE value set components. As illustrated in this diagram, the system comprises three layers: data integration, data access and quality evaluation. Data integration using a semantic web framework We converted the caDSR CDE data rendered in XML format into the RDF format using the XML2RDF web service API imple- mented in the ReDeFer project.19 We used 4store, a scalable open source RDF database developed at Garlik (Nottingham, Nottinghamshire, UK),21 as the data persistence layer, and accessed it via third-party Java client wrapper. Figure 3 shows a CDE example in the transformed RDF format. Once the CDE XML data were transformed into the RDF format, they were loaded into the RDF store by an import script. The NCIt was already rendered in RDF/OWL, so its contents were loaded directly into the RDF store using a built-in script. We used a third-part open source script22 to convert the UMLS SN into RDF format and loaded the contents into the RDF store. Data access using SPARQL queries With the RDF store loaded with the caDSR CDEs, the NCIt concepts and their semantic types, and the UMLS SN, we could Figure 2 System architecture of the semantic web infrastructure implemented for quality evaluation of common data element (CDE) value set components. caDSR, Cancer Data Standards Repository; OWL, web ontology language; RDF, resource description framework; TSV, tab separated values. e131