14,381 research outputs found
Introducing Dynamic Behavior in Amalgamated Knowledge Bases
The problem of integrating knowledge from multiple and heterogeneous sources
is a fundamental issue in current information systems. In order to cope with
this problem, the concept of mediator has been introduced as a software
component providing intermediate services, linking data resources and
application programs, and making transparent the heterogeneity of the
underlying systems. In designing a mediator architecture, we believe that an
important aspect is the definition of a formal framework by which one is able
to model integration according to a declarative style. To this purpose, the use
of a logical approach seems very promising. Another important aspect is the
ability to model both static integration aspects, concerning query execution,
and dynamic ones, concerning data updates and their propagation among the
various data sources. Unfortunately, as far as we know, no formal proposals for
logically modeling mediator architectures both from a static and dynamic point
of view have already been developed. In this paper, we extend the framework for
amalgamated knowledge bases, presented by Subrahmanian, to deal with dynamic
aspects. The language we propose is based on the Active U-Datalog language, and
extends it with annotated logic and amalgamation concepts. We model the sources
of information and the mediator (also called supervisor) as Active U-Datalog
deductive databases, thus modeling queries, transactions, and active rules,
interpreted according to the PARK semantics. By using active rules, the system
can efficiently perform update propagation among different databases. The
result is a logical environment, integrating active and deductive rules, to
perform queries and update propagation in an heterogeneous mediated framework.Comment: Other Keywords: Deductive databases; Heterogeneous databases; Active
rules; Update
Eliciting the Functional Taxonomy from protein annotations and taxa
The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules
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