Completing and Debugging Ontologies: state of the art and challenges

As semantically-enabled applications require high-quality ontologies, developing and maintaining ontologies that are as correct and complete as possible is an important although difficult task in ontology engineering. A key step is ontology debugging and completion. In general, there are two steps: detecting defects and repairing defects. In this paper we discuss the state of the art regarding the repairing step. We do this by formalizing the repairing step as an abduction problem and situating the state of the art with respect to this framework. We show that there are still many open research problems and show opportunities for further work and advancing the field.Comment: 56 page

Genetic Sequence Matching Using D4M Big Data Approaches

Recent technological advances in Next Generation Sequencing tools have led to increasing speeds of DNA sample collection, preparation, and sequencing. One instrument can produce over 600 Gb of genetic sequence data in a single run. This creates new opportunities to efficiently handle the increasing workload. We propose a new method of fast genetic sequence analysis using the Dynamic Distributed Dimensional Data Model (D4M) - an associative array environment for MATLAB developed at MIT Lincoln Laboratory. Based on mathematical and statistical properties, the method leverages big data techniques and the implementation of an Apache Acculumo database to accelerate computations one-hundred fold over other methods. Comparisons of the D4M method with the current gold-standard for sequence analysis, BLAST, show the two are comparable in the alignments they find. This paper will present an overview of the D4M genetic sequence algorithm and statistical comparisons with BLAST.Comment: 6 pages; to appear in IEEE High Performance Extreme Computing (HPEC) 201

Detecting and Correcting Conservativity Principle Violations in Ontology-to-Ontology Mappings

In order to enable interoperability between ontology-based systems, ontology matching techniques have been proposed. However, when the generated mappings suffer from logical flaws, their usefulness may be diminished. In this paper we present an approximate method to detect and correct violations to the so-called conservativity principle where novel subsumption entailments between named concepts in one of the input ontologies are considered as unwanted. We show that this is indeed the case in our application domain based on the EU Optique project. Additionally, our extensive evaluation conducted with both the Optique use case and the data sets from the Ontology Alignment Evaluation Initiative (OAEI) suggests that our method is both useful and feasible in practice.Copyright 2014 Springer International Publishing Switzerland. The final publication is available at http://link.springer.com/chapter/10.1007%2F978-3-319-11915-1_

Minimizing conservativity violations in ontology alignments: algorithms and evaluation

In order to enable interoperability between ontology-based systems, ontology matching techniques have been proposed. However, when the generated mappings lead to undesired logical consequences, their usefulness may be diminished. In this paper, we present an approach to detect and minimize the violations of the so-called conservativity principle where novel subsumption entailments between named concepts in one of the input ontologies are considered as unwanted. The practical applicability of the proposed approach is experimentally demonstrated on the datasets from the Ontology Alignment Evaluation Initiative

Uncovering Hidden Semantics of Set Information in Knowledge Bases

Knowledge Bases (KBs) contain a wealth of structured information about entities and predicates. This paper focuses on set-valued predicates, i.e., the relationship between an entity and a set of entities. In KBs, this information is often represented in two formats: (i) via counting predicates such as numberOfChildren and staffSize, that store aggregated integers, and (ii) via enumerating predicates such as parentOf and worksFor, that store individual set memberships. Both formats are typically complementary: unlike enumerating predicates, counting predicates do not give away individuals, but are more likely informative towards the true set size, thus this coexistence could enable interesting applications in question answering and KB curation. In this paper we aim at uncovering this hidden knowledge. We proceed in two steps. (i) We identify set-valued predicates from a given KB predicates via statistical and embedding-based features. (ii) We link counting predicates and enumerating predicates by a combination of co-occurrence, correlation and textual relatedness metrics. We analyze the prevalence of count information in four prominent knowledge bases, and show that our linking method achieves up to 0.55 F1 score in set predicate identification versus 0.40 F1 score of a random selection, and normalized discounted gains of up to 0.84 at position 1 and 0.75 at position 3 in relevant predicate alignments. Our predicate alignments are showcased in a demonstration system available at https://counqer.mpi-inf.mpg.de/spo