Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes

An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledge-based phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO, The Whole Brain Atlas and Neuronames, and allowed for complex queries such as “List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes”. Precision of the NLP-derived coding of the unstructured phenotypes in each dataset was 88% (n = 50), and precision of the semantic mapping between these terms across datasets was 98% (n = 100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets

Information Systems and Healthcare XVII: A HL7v3-based Mediating Schema Approach to Data Transfer between Heterogeneous Health Care Systems

One of the main challenges of exchanging patient care records between heterogeneous systems is the difficulty in overcoming semantic differences between them. This is further exacerbated by the lack of standardization in messaging protocols. As a solution to this problem, multiple ideas and standards have been proposed for exchanging clinical and administrative data in the healthcare area. However, most of these methods place some restrictions on the platform, standard or format, of the data. This paper proposes a context-specific, mediating schema-based architecture that enhances the transfer of electronic patient care records between healthcare information systems by using a reusable and portable model. The main contribution of this approach is its adaptability to a variety of schemas for the source and target systems

Intermediary XML schemas

The methodology of intermediary XML schemas is introduced and its application to complex metadata environments is explored. Intermediary schemas are designed to mediate to other ‘referent’ schemas: instances conforming to these are not generally intended for dissemination but must usually be realized by XSLT transformations for delivery. In some cases, these schemas may also generate instances conforming to themselves. Three subsidiary methods of this methodology are introduced. The first is application-specific schemas that act as intermediaries to established schemas which are problematic by virtue of their over-complexity or flexibility. The second employs the METS packaging standard as a template for navigating instances of a complex schema by defining an abstract map of its instances. The third employs the METS structural map to define templates or conceptual models from which instances of metadata for complex applications may be realized by XSLT transformations. The first method is placed in the context of earlier approaches to semantic interoperability such as crosswalks, switching across, derivation and application profiles. The second is discussed in the context of such methods for mapping complex objects as OAI-ORE and the Fedora Content Model Architecture. The third is examined in relation to earlier approaches to templating within XML architectures. The relevance of these methods to contemporary research is discussed in three areas: digital ecosystems, archival description and Linked Open Data in digital asset management and preservation. Their relevance to future research is discussed in the form of suggested enhancements to each, a possible synthesis of the second and third to overcome possible problems of interoperability presented by the first, and their potential role in future developments in digital preservation. This methodology offers an original approach to resolving issues of interoperability and the management of complex metadata environments; it significantly extends earlier techniques and does so entirely within XML architectures