Figure 4.

Annotation metadata. (A) An example illustrating the role of semantic metadata in support of the semantic interoperability for a set of DMRs. A key requisite is that the DMR metadata must make use of the same set of reference ontologies for its semantic content. Note how, in the case of the 'Reference List of Pathology Terms', a single element URI (yellow dot) is the subject of three distinct annotations to three ontology term URIs. In this particular example, a pathology entity is related to the (i) size quality of (ii) endothelial cells in (iii) the liver - linking the pathology entity URI via distinct relations to URIs respectively from PATO (biological qualities) [45], CellType [67] and FMA (gross anatomy) [29]. In the RICORDO infrastructure the Annotation Repository referred to in this diagram is implemented as an RDF Triple Store. (B) The DMR management architecture supports the querying of the repository of annotations using ontology terms as well as composites constructed ad hoc for a particular search. Query_1: Search for any annotation that involves ontology terms that are a type digestive organ by reasoning over the subsumption relations. This query takes as input the anatomy ontology URI for Digestive Organ (URI: 5). Results: (i) DMR [A] element that represents a pancreatic region on a CT image; (ii) DMR [C] element that bears a clinical trial vocabulary term; and (iii) DMR [E] element on the volume of the pancreas. Query_2: Search for annotations to all known vascular organs and their parts. This query takes as input the anatomy ontology URI for Vascular Organ (URI: 6) and returns: (i) DMR [B] element pertaining to the a surgical procedure report about the mitral valve; (ii) DMR [D] element for an cardiac echo Doppler; and (iii) DMR [F] for a medical record about the flow of blood from the patient's central veins to the right atrium. Query_3: 'Are there annotations that explicitly describe the size of organs?' The ad-hoc creation of a composite construct that refers to the size that pertains to all known organ subclasses and parts allows the RICORDO framework to ask this question. Results: DMR [D] as well as DMR [E]. Both 'Area' and 'Volume' are subclasses of 'Size' in the quality ontology. 'Pancreas' is a subclass of 'Organ', while 'Mitral Valve' is a part of the 'Organ' subclass 'Heart'.

de Bono et al. BMC Research Notes 2011 4:313   doi:10.1186/1756-0500-4-313
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