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

Application of Semantics to Solve Problems in Life Sciences

Fecha de lectura de Tesis: 10 de diciembre de 2018La cantidad de información que se genera en la Web se ha incrementado en los últimos años. La mayor parte de esta información se encuentra accesible en texto, siendo el ser humano el principal usuario de la Web. Sin embargo, a pesar de todos los avances producidos en el área del procesamiento del lenguaje natural, los ordenadores tienen problemas para procesar esta información textual. En este cotexto, existen dominios de aplicación en los que se están publicando grandes cantidades de información disponible como datos estructurados como en el área de las Ciencias de la Vida. El análisis de estos datos es de vital importancia no sólo para el avance de la ciencia, sino para producir avances en el ámbito de la salud. Sin embargo, estos datos están localizados en diferentes repositorios y almacenados en diferentes formatos que hacen difícil su integración. En este contexto, el paradigma de los Datos Vinculados como una tecnología que incluye la aplicación de algunos estándares propuestos por la comunidad W3C tales como HTTP URIs, los estándares RDF y OWL. Haciendo uso de esta tecnología, se ha desarrollado esta tesis doctoral basada en cubrir los siguientes objetivos principales: 1) promover el uso de los datos vinculados por parte de la comunidad de usuarios del ámbito de las Ciencias de la Vida 2) facilitar el diseño de consultas SPARQL mediante el descubrimiento del modelo subyacente en los repositorios RDF 3) crear un entorno colaborativo que facilite el consumo de Datos Vinculados por usuarios finales, 4) desarrollar un algoritmo que, de forma automática, permita descubrir el modelo semántico en OWL de un repositorio RDF, 5) desarrollar una representación en OWL de ICD-10-CM llamada Dione que ofrezca una metodología automática para la clasificación de enfermedades de pacientes y su posterior validación haciendo uso de un razonador OWL

The anatomy of phenotype ontologies: principles, properties and applications

The past decade has seen an explosion in the collection of genotype data in domains as diverse as medicine, ecology, livestock and plant breeding. Along with this comes the challenge of dealing with the related phenotype data, which is not only large but also highly multidimensional. Computational analysis of phenotypes has therefore become critical for our ability to understand the biological meaning of genomic data in the biological sciences. At the heart of computational phenotype analysis are the phenotype ontologies. A large number of these ontologies have been developed across many domains, and we are now at a point where the knowledge captured in the structure of these ontologies can be used for the integration and analysis of large interrelated data sets. The Phenotype And Trait Ontology framework provides a method for formal definitions of phenotypes and associated data sets and has proved to be key to our ability to develop methods for the integration and analysis of phenotype data. Here, we describe the development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally.The National Science Foundation (IOS:1340112 to G.V.G.), the European Commission H2020 (grant agreement number 731075) to G.V.G. and the King Abdullah University of Science and Technology (to R.H.)

Fast modularisation and aomic decomposition of ontologies using axiom dependency hypergraphs

In this paper we define the notion of an axiom dependency hypergraph, which explicitly represents how axioms are included into a module by the algorithm for computing locality-based modules. A locality-based module of an ontology corresponds to a set of connected nodes in the hypergraph, and atoms of an ontology to strongly connected components. Collapsing the strongly connected components into single nodes yields a condensed hypergraph that comprises a representation of the atomic decomposition of the ontology. To speed up the condensation of the hypergraph, we first reduce its size by collapsing the strongly connected components of its graph fragment employing a linear time graph algorithm. This approach helps to significantly reduce the time needed for computing the atomic decomposition of an ontology. We provide an experimental evaluation for computing the atomic decomposition of large biomedical ontologies. We also demonstrate a significant improvement in the time needed to extract locality-based modules from an axiom dependency hypergraph and its condensed version

Enhancing Automated Decision Support across Medical and Oral Health Domains with Semantic Web Technologies

Research has shown that the general health and oral health of an individual are closely related. Accordingly, current practice of isolating the information base of medical and oral health domains can be dangerous and detrimental to the health of the individual. However, technical issues such as heterogeneous data collection and storage formats, limited sharing of patient information and lack of decision support over the shared information are the principal reasons for the current state of affairs. To address these issues, the following research investigates the development and application of a cross-domain ontology and rules to build an evidence-based and reusable knowledge base consisting of the inter-dependent conditions from the two domains. Through example implementation of the knowledge base in Protege, we demonstrate the effectiveness of our approach in reasoning over and providing decision support for cross-domain patient information.Comment: The paper has been published at the 24th Australasian Conference on Information Systems, 4-6 Dec 2013, Melbourne. The paper can be found at: http://mo.bf.rmit.edu.au/acis2013/382.pd

Maintaining Integrity Constraints in Semantic Web

As an expressive knowledge representation language for Semantic Web, Web Ontology Language (OWL) plays an important role in areas like science and commerce. The problem of maintaining integrity constraints arises because OWL employs the Open World Assumption (OWA) as well as the Non-Unique Name Assumption (NUNA). These assumptions are typically suitable for representing knowledge distributed across the Web, where the complete knowledge about a domain cannot be assumed, but make it challenging to use OWL itself for closed world integrity constraint validation. Integrity constraints (ICs) on ontologies have to be enforced; otherwise conflicting results would be derivable from the same knowledge base (KB). The current trends of incorporating ICs into OWL are based on its query language SPARQL, alternative semantics, or logic programming. These methods usually suffer from limited types of constraints they can handle, and/or inherited computational expensiveness. This dissertation presents a comprehensive and efficient approach to maintaining integrity constraints. The design enforces data consistency throughout the OWL life cycle, including the processes of OWL generation, maintenance, and interactions with other ontologies. For OWL generation, the Paraconsistent model is used to maintain integrity constraints during the relational database to OWL translation process. Then a new rule-based language with set extension is introduced as a platform to allow users to specify constraints, along with a demonstration of 18 commonly used constraints written in this language. In addition, a new constraint maintenance system, called Jena2Drools, is proposed and implemented, to show its effectiveness and efficiency. To further handle inconsistencies among multiple distributed ontologies, this work constructs a framework to break down global constraints into several sub-constraints for efficient parallel validation