Characteristic sets profile features: Estimation and application to SPARQL query planning

RDF dataset profiling is the task of extracting a formal representation of a dataset’s features. Such features may cover various aspects of the RDF dataset ranging from information on licensing and provenance to statistical descriptors of the data distribution and its semantics. In this work, we focus on the characteristics sets profile features that capture both structural and semantic information of an RDF dataset, making them a valuable resource for different downstream applications. While previous research demonstrated the benefits of characteristic sets in centralized and federated query processing, access to these fine-grained statistics is taken for granted. However, especially in federated query processing, computing this profile feature is challenging as it can be difficult and/or costly to access and process the entire data from all federation members. We address this shortcoming by introducing the concept of a profile feature estimation and propose a sampling-based approach to generate estimations for the characteristic sets profile feature. In addition, we showcase the applicability of these feature estimations in federated querying by proposing a query planning approach that is specifically designed to leverage these feature estimations. In our first experimental study, we intrinsically evaluate our approach on the representativeness of the feature estimation. The results show that even small samples of just 0.5% of the original graph’s entities allow for estimating both structural and statistical properties of the characteristic sets profile features. Our second experimental study extrinsically evaluates the estimations by investigating their applicability in our query planner using the well-known FedBench benchmark. The results of the experiments show that the estimated profile features allow for obtaining efficient query plans

Applying the functional abnormality ontology pattern to anatomical functions.

BACKGROUND: Several biomedical ontologies cover the domain of biological functions, including molecular and cellular functions. However, there is currently no publicly available ontology of anatomical functions. Consequently, no explicit relation between anatomical structures and their functions is expressed in the anatomy ontologies that are available for various species. Such an explicit relation between anatomical structures and their functions would be useful both for defining the classes of the anatomy and the phenotype ontologies accurately. RESULTS: We provide an ontological analysis of functions and functional abnormalities. From this analysis, we derive an approach to the automatic extraction of anatomical functions from existing ontologies which uses a combination of natural language processing, graph-based analysis of the ontologies and formal inferences. Additionally, we introduce a new relation to link material objects to processes that realize the function of these objects. This relation is introduced to avoid a needless duplication of processes already covered by the Gene Ontology in a new ontology of anatomical functions. CONCLUSIONS: Ontological considerations on the nature of functional abnormalities and their representation in current phenotype ontologies show that we can extract a skeleton for an ontology of anatomical functions by using a combination of process, phenotype and anatomy ontologies automatically. We identify several limitations of the current ontologies that still need to be addressed to ensure a consistent and complete representation of anatomical functions and their abnormalities. AVAILABILITY: The source code and results of our analysis are available at http://bioonto.de