Functional and Efficient Query Interpreters: Principle, Application and Performances’ Comparison

This paper presents a general approach to implement efficient queries’ interpreters in a functional programming language. Indeed, most of the standard tools actually available use an imperative and/or object-oriented language for the implementation (e.g. Java for Jena-Fuseki) but other paradigms are possible with, maybe, better performances. To proceed, the paper first explains how to model data structures and queries in a functional point of view. Then, it proposes a general methodology to get performances (i.e. number of computation steps to answer a query) then it explains how to integrate some optimization techniques (short-cut fusion and, more important, data transformations). It then compares the functional server proposed to a standard tool (Fuseki) demonstrating that the first one can be twice to ten times faster to answer queries

Categorical Models for BigData

This paper shows how concepts coming from category theory associated to a functional programming language can help to formalize and reason about data and get efficient programs in a BigData context. More precisely, it shows how data structures can be modeled by functors related by natural transformations (and isomorphisms). The transformation functions can then serve to shift a data structure and then get another program (eventually educing time complexity). The paper then explains the main concepts of the theory, how to apply them and gives an application to a concrete database and the performances obtained

Approche formelle de fusion d'ontologies à l'aide des grammaires de graphes typés

L'article propose une approche formelle de fusion d'ontologies se reposant sur les grammaires de graphes typés. Elle se décompose en trois étapes : 1) la recherche de similarités entre concepts ; 2) la fusion des ontologies par l'approche algébrique SPO (Simple Push Out) ; 3) l'adaptation d'une ontologie globale par le biais de règles de réécriture de graphes. Contrairement aux solutions existantes, cette méthode offre une représentation formelle de la fusion d'ontologies ainsi qu'une implémentation fonctionnelle basée sur l'outil AGG

Algebraic graph transformations for merging ontologies

The conception of an ontology is a complex task influenced by numerous factors like the point of view of the authors or the level of details. Consequently, several ontologies have been developed to model identical or related domains leading to partially overlapping representations. This divergence of conceptualization requires the study of ontologies merging in order to create a common repository of knowledge and integrate various sources of information. In this paper, we propose a formal approach for merging ontologies using typed graph grammars. This method relies on the algebraic approach to graph transformations, SPO (Simple PushOut) which allows a formal representation and ensures the consistence of the results. Furthermore, a new ontologies merging algorithm called GROM (Graph Rewriting for Ontology Merging) is presented

Algebraic graph transformations for formalizing ontology changes and evolving ontologies

An ontology represents a consensus on the representation of the concepts and axioms of a given domain. This consensus is often reached through an iterative process, each iteration consisting in modifying the current version of the consensus. Furthermore, frequent and continuous changes are also occurring when the represented domain evolves or when new requirements have to be considered. Consequently, ontologies have to be adaptable to handle evolution, revision and refinement. However, this process is highly challenging as it is often difficult to understand all affected ontology parts when changes are performed. Thus, inconsistencies can occur in the ontology as the changes can introduce contradictory axioms. To address this issue, this paper presents a formal approach for evolving ontologies using Typed Graph Grammars. This method relies on the algebraic approach Simple PushOut (SPO) of graph transformations. It formalizes the ontology changes and proposes an a priori approach of inconsistencies resolution. The modified ontology does not need an explicit checking as an incorrect ontology version cannot actually be generated. To validate our proposal, an implementation is presented using the Attributed Graph Grammar (AGG) toolbox

Consistent Ontologies Evolution Using Graph Grammars

Ontologies are often used for the meta-modelling of dynamic domains, therefore it is essential to represent and manage their changes and to adapt them to new requirements. Due to changes, an ontology may become invalid and non-interpretable. This paper proposes the use of the graph grammars to formalize and manage ontologies evolution. The objective is to present an a priori approach of inconsistencies resolutions to adapt the ontologies and preserve their consistency. A framework composed of different graph rewriting rules is proposed and presented using the AGG (Algebraic Graph Grammar) tool. As an application, the article considers the EventCCAlps ontology developed within the CCAlps European project

Big metamodels are evil

While reuse is typically considered a good practice, it may also lead to keeping irrelevant concerns in derived elements. For instance, new metamodels are usually built upon existing metamodels using additive techniques such as profiling and package merge. With such additive techniques, new metamodels tend to become bigger and bigger, which leads to harmful overheads of complexity for both tool builders and users. In this paper, we introduce ≪ package unmerge≫ - a proposal for a subtractive relation between packages - which complements existing metamodel-extension techniques

Antibody Evasion by a Gammaherpesvirus O-Glycan Shield

All gammaherpesviruses encode a major glycoprotein homologous to the Epstein-Barr virus gp350. These glycoproteins are often involved in cell binding, and some provide neutralization targets. However, the capacity of gammaherpesviruses for long-term transmission from immune hosts implies that in vivo neutralization is incomplete. In this study, we used Bovine Herpesvirus 4 (BoHV-4) to determine how its gp350 homolog - gp180 - contributes to virus replication and neutralization. A lack of gp180 had no impact on the establishment and maintenance of BoHV-4 latency, but markedly sensitized virions to neutralization by immune sera. Antibody had greater access to gB, gH and gL on gp180-deficient virions, including neutralization epitopes. Gp180 appears to be highly O-glycosylated, and removing O-linked glycans from virions also sensitized them to neutralization. It therefore appeared that gp180 provides part of a glycan shield for otherwise vulnerable viral epitopes. Interestingly, this O-glycan shield could be exploited for neutralization by lectins and carbohydrate-specific antibody. The conservation of O-glycosylation sites in all gp350 homologs suggests that this is a general evasion mechanism that may also provide a therapeutic target

Adaptation consistante d'ontologies à l'aide des grammaires de graphes

Les ontologies tendent à intégrer le cœur de tout système d'information. Les domaines évoluant sans cesse, les ontologies doivent elles même pouvoir s'adapter. Dans ce contexte, l'article propose la formalisation du concept d'adaptation basée sur les grammaires de graphes, ce qui permet notamment de gérer les changements des ontologies et de définir une approche à priori de résolution des incohérences susceptibles d'être générées. Comme application, l'article considère l'ontologie EventCCAlps développée dans le cadre du projet européen CCAlps

Antibodies against bovine herpesvirus 4 are highly prevalent in wild African buffaloes throughout eastern and southern Africa

Bovine herpesvirus 4 (BoHV-4) has been isolated from cattle throughout the world. Interestingly, a survey of wild African buffaloes mainly from the Maasai Mara Game Reserve in Kenya revealed that 94% of the animals tested had anti-BoHV-4 antibodies [Rossiter, P.B., Gumm, I.D., Stagg, D.A., Conrad, PA., Mukolwe, S., Davies, F.G., White, H., 1989. Isolation of bovine herpesvirus-3 from African buffaloes (Syncerus caffer). Res. Vet. Sci. 46, 337-343]. These authors also proposed that the serological antigenic relationship existing between BoHV-4 and alcelaphine herpesvirus I (A1HV-1) could confer to BoHV-4 infected buffaloes a protective immune response against lethal A1HV-1 infection. In the present study, we addressed two questions related to Rossiter et al. paper. Firstly, to investigate the role of the African buffalo as a natural host species of BoHV-4, the seroprevalence of anti-BoHV-4 antibodies was analysed in wild African buffaloes throughout eastern and southern Africa. A total of 400 sera was analysed using two complementary immunofluorescent assays. These analyses revealed that independently of their geographical origin, wild African buffaloes exhibit a seroprevalence of anti-BoHV-4 antibodies higher than 68%. This result is by far above the seroprevalence generally observed in cattle. Our data are discussed in the light of our recent phylogenetic study demonstrating that the BoHV-4 Bo17 gene has been acquired from a recent ancestor of the African buffalo. Secondly, we investigated the humoral antigenic relationship existing between BoHV-4 and A1HV-1. Our results demonstrate that among the antigens expressed in A1HV-1 infected cells, epitope(s) recognised by anti-BoHV-4 antibodies are exclusively nuclear, suggesting that the putative property of BoHV-4 to confer an immune protection against A1HV-1 relies on a cellular rather than on a humoral immune response. (c) 2005 Elsevier B.V. All rights reserved