Related papers: Mapping Data to Ontologies with Exceptions Using A…
We present a categorical denotational semantics for a database mapping, based on views, in the most general framework of a database integration/exchange. Developed database category DB, for databases (objects) and view-based mappings…
The paper introduces the notion of off-line justification for Answer Set Programming (ASP). Justifications provide a graph-based explanation of the truth value of an atom w.r.t. a given answer set. The paper extends also this notion to…
Ontology-based data integration has been one of the practical methodologies for heterogeneous legacy database integrated service construction. However, it is neither efficient nor economical to build the cross-domain ontology on top of the…
In the context of the model-driven development of data-centric applications, OCL constraints play a major role in adding precision to the source models (e.g., data models and security models). Several code-generators have been proposed to…
Stratifying cancer patients based on their gene expression levels allows improving diagnosis, survival analysis and treatment planning. However, such data is extremely highly dimensional as it contains expression values for over 20000 genes…
Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases…
Trees -- i.e., the type of data structure known under this name -- are central to many aspects of knowledge organization. We investigate some central design choices concerning the ontological modeling of such trees. In particular, we…
We study the problem of rewriting an ontology O1 expressed in a DL L1 into an ontology O2 in a Horn DL L2 such that O1 and O2 are equisatisfiable when extended with an arbitrary dataset. Ontologies that admit such rewritings are amenable to…
Magic sets are a Datalog to Datalog rewriting technique to optimize query answering. The rewritten program focuses on a portion of the stable model(s) of the input program which is sufficient to answer the given query. However, the…
This paper discusses the representation of ontologies in the first-order logical environment {\ttfamily FOLE}. An ontology defines the primitives with which to model the knowledge resources for a community of discourse. These primitives…
Our broader goal is to automatically translate English sentences into formulas in appropriate knowledge representation languages as a step towards understanding and thus answering questions with respect to English text. Our focus in this…
We introduce novel mathematical models and algorithms to generate (shortest or k different) explanations for biomedical queries, using answer set programming. We implement these algorithms and integrate them in BIOQUERY-ASP. We illustrate…
Ontology, and more broadly, Knowledge Graph Matching is a challenging task in which expressiveness has not been fully addressed. Despite the increasing use of embeddings and language models for this task, approaches for generating…
We examine the practicality for a user of using Answer Set Programming (ASP) for representing logical formalisms. We choose as an example a formalism aiming at capturing causal explanations from causal information. We provide an…
Answer Set Programming (ASP) is a declarative programming paradigm based on logic programming and non-monotonic reasoning. It is a tremendously powerful tool for describing and solving combinatorial problems. Like any other language, ASP…
The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such caGrid, support access…
This paper is about Kripke structures that are inside a relational database and queried with a modal language. At first the modal language that is used is introduced, followed by a definition of the database and relational algebra. Based on…
Ontologies are known for their ability to organize rich metadata, support the identification of novel insights via semantic queries, and promote reuse. In this paper, we consider the problem of automated planning, where the objective is to…
The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies.…
Relational and noSQL storages are developed for the fast processing of the large data sets having a stable structure, while the ontologies are used to rep-resent complex and dynamic sets of information of a limited size. In the in-dustrial…