Investigating subsumption in DL-based terminologies: A case study in SNOMED CT

Formalisms such as description logics (DL) are sometimes expected to help terminologies ensure compliance with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) complies with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of the classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with multiple inheritance

Reasoning with Individuals for the Description Logic SHIQ

While there has been a great deal of work on the development of reasoning algorithms for expressive description logics, in most cases only Tbox reasoning is considered. In this paper we present an algorithm for combined Tbox and Abox reasoning in the SHIQ description logic. This algorithm is of particular interest as it can be used to decide the problem of (database) conjunctive query containment w.r.t. a schema. Moreover, the realisation of an efficient implementation should be relatively straightforward as it can be based on an existing highly optimised implementation of the Tbox algorithm in the FaCT system.Comment: To appear at CADE-1

Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-Based Biomedical Terminologies

Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED CT classes with respect to these principles. Our major results are: 31% of these classes have a single child; 27% have multiple parents; 51% do not exhibit any differentiae between the description of the parent and that of the child. The applications of this study to quality assurance for ontologies are discussed and suggestions are made for dealing with the phenomenon of multiple inheritance. The advantages and limitations of our approach are also discussed

Spatial location and its relevance for terminological inferences in bio-ontologies

<p>Abstract</p> <p>Background</p> <p>An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of physical aggregation and containment.</p> <p>Results</p> <p>We demonstrate that the proposed formalism allows to deal consistently with "role propagation along non-taxonomic hierarchies", a problem which had repeatedly been identified as an intricate reasoning problem in biomedical ontologies.</p> <p>Conclusion</p> <p>The proposed approach seems to be suitable for the redesign of compositional hierarchies in (bio)medical terminology systems which are embedded into the framework of the OBO (Open Biological Ontologies) Relation Ontology and are using knowledge representation languages developed by the Semantic Web community.</p

Representación de conocimiento: las lógicas descriptivas en un enfoque orientado a objetos

La representación de conocimiento es una de las actividades más atrayentes de la Inteligencia Artificial (Artificial Intelligence: AI), para poder abstraer el saber es necesario tener en cuenta aspectos importantes como el conocimiento de la estructura del lenguaje en que se especifica y el proceso de análisis que se debe aplicar a este lenguaje, las Lógicas descriptivas (Description Logics DLs) en el enfoque orientado a objetos nos permiten obtener un formalismo óptimo para la representación, tomando los conceptos del mundo real en que se apoya nuestro conocimiento y las relaciones (roles) entre conceptos, todo esto ayudado con un conjunto de constructores lógicos para completar una expresividad adecuada a los requerimientos del que expresa

Module extraction for inexpressive description logics

Module extraction is an important reasoning task, aiding in the design, reuse and maintenance of ontologies. Reasoning services such as subsumption testing and MinA extraction have been shown to bene t from module extraction methods. Though various syntactic traversal-based module extraction algorithms exist for extracting modules, many only consider the subsumee of a subsumption statement as a selection criterion for reducing the axioms in the module. In this dissertation we extend the bottom-up reachability-based module extraction heuristic for the inexpressive Description Logic EL, by introducing a top-down version of the heuristic which utilises the subsumer of a subsumption statement as a selection criterion to minimize the number of axioms in a module. Then a combined bidirectional heuristic is introduced which uses both operands of a subsumption statement in order to extract very small modules. We then investigate the relationship between MinA extraction and bidirectional reachabilitybased module extraction. We provide empirical evidence that bidirectional reachability-based module extraction for subsumption entailments in EL provides a signi cant reduction in the size of modules for almost no additional costs in the running time of the original algorithms.Computer ScienceM. Sc. (Computer Science

Polynomial-Time Reasoning Support for Design and Maintenance of Large-Scale Biomedical Ontologies

Description Logics (DLs) belong to a successful family of knowledge representation formalisms with two key assets: formally well-defined semantics which allows to represent knowledge in an unambiguous way and automated reasoning which allows to infer implicit knowledge from the one given explicitly. This thesis investigates various reasoning techniques for tractable DLs in the EL family which have been implemented in the CEL system. It suggests that the use of the lightweight DLs, in which reasoning is tractable, is beneficial for ontology design and maintenance both in terms of expressivity and scalability. The claim is supported by a case study on the renown medical ontology SNOMED CT and extensive empirical evaluation on several large-scale biomedical ontologies

A Description Logic Based Schema for the Classification of Medical Data

The European Galen project aims to promote the sharing and re-use of medical data by providing a concept model which can be used by application designers as a flexible and extensible classification schema. A description logic style terminological knowledge representation system called Grail has been developed specifically for this task. Using a description logic based schema has a number of important benefits including coherence checking, schema enrichment and query optimisation. In order to support a variety of design requirements Grail includes transitive closure of roles and general concept inclusions. Replacing the Grail classifier’s existing structural subsumption algorithm with a sound, provably complete and decidable tableaux calculus based algorithm would have many attractions if the intractability problem could be mitigated by suitable optimisations. The optimisation of non-deterministic constraint expansion would be of particular importance as large numbers of these constraints can be introduced by general concept inclusions. Both intelligent back-tracking and the use of meta-knowledge to guide constraint expansion are being studied as possible methods of tackling this problem