Efficient Discovery of Ontology Functional Dependencies

Poor data quality has become a pervasive issue due to the increasing complexity and size of modern datasets. Constraint based data cleaning techniques rely on integrity constraints as a benchmark to identify and correct errors. Data values that do not satisfy the given set of constraints are flagged as dirty, and data updates are made to re-align the data and the constraints. However, many errors often require user input to resolve due to domain expertise defining specific terminology and relationships. For example, in pharmaceuticals, 'Advil' \emph{is-a} brand name for 'ibuprofen' that can be captured in a pharmaceutical ontology. While functional dependencies (FDs) have traditionally been used in existing data cleaning solutions to model syntactic equivalence, they are not able to model broader relationships (e.g., is-a) defined by an ontology. In this paper, we take a first step towards extending the set of data quality constraints used in data cleaning by defining and discovering \emph{Ontology Functional Dependencies} (OFDs). We lay out theoretical and practical foundations for OFDs, including a set of sound and complete axioms, and a linear inference procedure. We then develop effective algorithms for discovering OFDs, and a set of optimizations that efficiently prune the search space. Our experimental evaluation using real data show the scalability and accuracy of our algorithms.Comment: 12 page

International Veterinary Epilepsy Task Force consensus proposal: Medical treatment of canine epilepsy in Europe

In Europe, the number of antiepileptic drugs (AEDs) licensed for dogs has grown considerably over the last years. Nevertheless, the same questions remain, which include, 1) when to start treatment, 2) which drug is best used initially, 3) which adjunctive AED can be advised if treatment with the initial drug is unsatisfactory, and 4) when treatment changes should be considered. In this consensus proposal, an overview is given on the aim of AED treatment, when to start long-term treatment in canine epilepsy and which veterinary AEDs are currently in use for dogs. The consensus proposal for drug treatment protocols, 1) is based on current published evidence-based literature, 2) considers the current legal framework of the cascade regulation for the prescription of veterinary drugs in Europe, and 3) reflects the authors’ experience. With this paper it is aimed to provide a consensus for the management of canine idiopathic epilepsy. Furthermore, for the management of structural epilepsy AEDs are inevitable in addition to treating the underlying cause, if possible

Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania

Hybrid genotypes have been repeatedly described among natural isolates of Leishmania, and the recovery of experimental hybrids from sand flies co-infected with different strains or species of Leishmania has formally demonstrated that members of the genus possess the machinery for genetic exchange. As neither gamete stages nor cell fusion events have been directly observed during parasite development in the vector, we have relied on a classical genetic analysis to determine if Leishmania has a true sexual cycle. Here, we used whole genome sequencing to follow the chromosomal inheritance patterns of experimental hybrids generated within and between different strains of L. major and L. infantum. We also generated and sequenced the first experimental hybrids in L. tropica. We found that in each case the parental somy and allele contributions matched the inheritance patterns expected under meiosis 97–99% of the time. The hybrids were equivalent to F1 progeny, heterozygous throughout most of the genome for the markers that were homozygous and different between the parents. Rare, non-Mendelian patterns of chromosomal inheritance were observed, including a gain or loss of somy, and loss of heterozygosity, that likely arose during meiosis or during mitotic divisions of the progeny clones in the fly or culture. While the interspecies hybrids appeared to be sterile, the intraspecies hybrids were able to produce backcross and outcross progeny. Analysis of 5 backcross and outcross progeny clones generated from an L. major F1 hybrid, as well as 17 progeny clones generated from backcrosses involving a natural hybrid of L. tropica, revealed genome wide patterns of recombination, demonstrating that classical crossing over occurs at meiosis, and allowed us to construct the first physical and genetic maps in Leishmania. Altogether, the findings provide strong evidence for meiosis-like sexual recombination in Leishmania, presenting clear opportunities for forward genetic analysis and positional cloning of important genes.</div

Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better

Joel Cohen offers a historical and prospective analysis of the relationship between mathematics and biolog

Horizontal Integration of Warfighter Intelligence Data: A Shared Semantic Resource for the Intelligence Community

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts