Methods Inf Med - Toward a view-oriented approach for aligning RDF-based biomedical repositories.


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TRODUCTION: This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems".BACKGROUND: The need for complementary access to multiple RDF databases has fostered new lines of research, but also entailed new challenges due to data representation disparities. While several approaches for RDF-based database integration have been proposed, those focused on schema alignment have become the most widely adopted. All state-of-the-art solutions for aligning RDF-based sources resort to a simple technique inherited from legacy relational database integration methods. This technique - known as element-to-element (e2e) mappings - is based on establishing 1:1 mappings between single primitive elements - e.g. concepts, attributes, relationships, etc. - belonging to the source and target schemas. However, due to the intrinsic nature of RDF - a representation language based on defining tuples < subject, predicate, object > -, one may find RDF elements whose semantics vary dramatically when combined into a view involving other RDF elements - i.e. they depend on their context. The latter cannot be adequately represented in the target schema by resorting to the traditional e2e approach. These approaches fail to properly address this issue without explicitly modifying the target ontology, thus lacking the required expressiveness for properly reflecting the intended semantics in the alignment information.OBJECTIVES: To enhance existing RDF schema alignment techniques by providing a mechanism to properly represent elements with context-dependent semantics, thus enabling users to perform more expressive alignments, including scenarios that cannot be adequately addressed by the existing approaches.METHODS: Instead of establishing 1:1 correspondences between single primitive elements of the schemas, we propose adopting a view-based approach. The latter is targeted at establishing mapping relationships between RDF subgraphs - that can be regarded as the equivalent of views in traditional databases -, rather than between single schema elements. This approach enables users to represent scenarios defined by context-dependent RDF elements that cannot be properly represented when adopting the currently existing approaches.RESULTS: We developed a software tool implementing our view-based strategy. Our tool is currently being used in the context of the European Commission funded p-medicine project, targeted at creating a technological framework to integrate clinical and genomic data to facilitate the development of personalized drugs and therapies for cancer, based on the genetic profile of the patient. We used our tool to integrate different RDF-based databases - including different repositories of clinical trials and DICOM images - using the Health Data Ontology Trunk (HDOT) ontology as the target schema.CONCLUSIONS: The importance of database integration methods and tools in the context of biomedical research has been widely recognized. Modern research in this area - e.g. identification of disease biomarkers, or design of personalized therapies - heavily relies on the availability of a technical framework to enable researchers to uniformly access disparate repositories. We present a method and a tool that implement a novel alignment method specifically designed to support and enhance the integration of RDF-based data sources at schema (metadata) level. This approach provides an increased level of expressiveness compared to other existing solutions, and allows solving heterogeneity scenarios that cannot be properly represented using other state-of-the-art techniques.

Resumo Limpo

troduct articl part focus theme method inform medicin manag interoper complex health systemsbackground need complementari access multipl rdf databas foster new line research also entail new challeng due data represent dispar sever approach rdfbase databas integr propos focus schema align becom wide adopt stateoftheart solut align rdfbase sourc resort simpl techniqu inherit legaci relat databas integr method techniqu known elementtoel ee map base establish map singl primit element eg concept attribut relationship etc belong sourc target schema howev due intrins natur rdf represent languag base defin tupl subject predic object one may find rdf element whose semant vari dramat combin view involv rdf element ie depend context latter adequ repres target schema resort tradit ee approach approach fail proper address issu without explicit modifi target ontolog thus lack requir express proper reflect intend semant align informationobject enhanc exist rdf schema align techniqu provid mechan proper repres element contextdepend semant thus enabl user perform express align includ scenario adequ address exist approachesmethod instead establish correspond singl primit element schema propos adopt viewbas approach latter target establish map relationship rdf subgraph can regard equival view tradit databas rather singl schema element approach enabl user repres scenario defin contextdepend rdf element proper repres adopt current exist approachesresult develop softwar tool implement viewbas strategi tool current use context european commiss fund pmedicin project target creat technolog framework integr clinic genom data facilit develop person drug therapi cancer base genet profil patient use tool integr differ rdfbase databas includ differ repositori clinic trial dicom imag use health data ontolog trunk hdot ontolog target schemaconclus import databas integr method tool context biomed research wide recogn modern research area eg identif diseas biomark design person therapi heavili reli avail technic framework enabl research uniform access dispar repositori present method tool implement novel align method specif design support enhanc integr rdfbase data sourc schema metadata level approach provid increas level express compar exist solut allow solv heterogen scenario proper repres use stateoftheart techniqu

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