Ontology based Clinical Practice Justification in Natural Language

One of the most important contributions that any decision support system can make to achieve wide acceptance among any community is to be able to justify its own suggestions. When dealing with highly technical and scientifically advanced practitioners like medical doctors or any other related clinical workers, the ability to justify itself using the domain specialist usual terminology and technicalities is imperative. In this article we demonstrate the use of an ontological framework as inferencing basis for automatic sound clinical suggestions providing. Our work has two main contributions, consolidating the use of \{OGCP\} (Ontology for General Clinical Practice) as foundation and providing controlled English justifications of the extracted suggestions. We found that clinical practitioners feel as acceptable the Attempto Controlled English justifications generated from the knowledge base

Using structural and semantic methodologies to enhance biomedical terminologies

Biomedical terminologies and ontologies underlie various Health Information Systems (HISs), Electronic Health Record (EHR) Systems, Health Information Exchanges (HIEs) and health administrative systems. Moreover, the proliferation of interdisciplinary research efforts in the biomedical field is fueling the need to overcome terminological barriers when integrating knowledge from different fields into a unified research project. Therefore well-developed and well-maintained terminologies are in high demand. Most of the biomedical terminologies are large and complex, which makes it impossible for human experts to manually detect and correct all errors and inconsistencies. Automated and semi-automated Quality Assurance methodologies that focus on areas that are more likely to contain errors and inconsistencies are therefore important. In this dissertation, structural and semantic methodologies are used to enhance biomedical terminologies. The dissertation work is divided into three major parts. The first part consists of structural auditing techniques for the Semantic Network of the Unified Medical Language System (UMLS), which serves as a vocabulary knowledge base for biomedical research in various applications. Research techniques are presented on how to automatically identify and prevent erroneous semantic type assignments to concepts. The Web-based adviseEditor system is introduced to help UMLS editors to make correct multiple semantic type assignments to concepts. It is made available to the National Library of Medicine for future use in maintaining the UMLS. The second part of this dissertation is on how to enhance the conceptual content of SNOMED CT by methods of semantic harmonization. By 2015, SNOMED will become the standard terminology for EH R encoding of diagnoses and problem lists. In order to enrich the semantics and coverage of SNOMED CT for clinical and research applications, the problem of semantic harmonization between SNOMED CT and six reference terminologies is approached by 1) comparing the vertical density of SNOM ED CT with the reference terminologies to find potential concepts for export and import; and 2) categorizing the relationships between structurally congruent concepts from pairs of terminologies, with SNOMED CT being one terminology in the pair. Six kinds of configurations are observed, e.g., alternative classifications, and suggested synonyms. For each configuration, a corresponding solution is presented for enhancing one or both of the terminologies. The third part applies Quality Assurance techniques based on “Abstraction Networks” to biomedical ontologies in BioPortal. The National Center for Biomedical Ontology provides B ioPortal as a repository of over 350 biomedical ontologies covering a wide range of domains. It is extremely difficult to design a new Quality Assurance methodology for each ontology in BioPortal. Fortunately, groups of ontologies in BioPortal share common structural features. Thus, they can be grouped into families based on combinations of these features. A uniform Quality Assurance methodology design for each family will achieve improved efficiency, which is critical with the limited Quality Assurance resources available to most ontology curators. In this dissertation, a family-based framework covering 186 BioPortal ontologies and accompanying Quality Assurance methods based on abstraction networks are presented to tackle this problem

Truth maintenance in knowledge-based systems

Truth Maintenance Systems (TMS) have been applied in a wide range of domains, from diagnosing electric circuits to belief revision in agent systems. There also has been work on using the TMS in modern Knowledge-Based Systems such as intelligent agents and ontologies. This thesis investigates the applications of TMSs in such systems. For intelligent agents, we use a “light-weight” TMS to support query caching in agent programs. The TMS keeps track of the dependencies between a query and the facts used to derive it so that when the agent updates its database, only affected queries are invalidated and removed from the cache. The TMS employed here is “light-weight” as it does not maintain all intermediate reasoning results. Therefore, it is able to reduce memory consumption and to improve performance in a dynamic setting such as in multi-agent systems. For ontologies, this work extends the Assumption-based Truth Maintenance System (ATMS) to tackle the problem of axiom pinpointing and debugging in ontology-based systems with different levels of expressivity. Starting with finding all errors in auto-generated ontology mappings using a “classic” ATMS [23], we extend the ATMS to solve the axiom pinpointing problem in Description Logics-based Ontologies. We also attempt this approach to solve the axiom pinpointing problem in a more expressive upper ontology, SUMO, whose underlying logic is undecidable

Practical reasoning for defeasable description logics.

Doctor of Philosophy in Mathematics, Statistics and Computer Science. University of KwaZulu-Natal, Durban 2016.Description Logics (DLs) are a family of logic-based languages for formalising ontologies. They have useful computational properties allowing the development of automated reasoning engines to infer implicit knowledge from ontologies. However, classical DLs do not tolerate exceptions to speci ed knowledge. This led to the prominent research area of nonmonotonic or defeasible reasoning for DLs, where most techniques were adapted from seminal works for propositional and rst-order logic. Despite the topic's attention in the literature, there remains no consensus on what \sensible" defeasible reasoning means for DLs. Furthermore, there are solid foundations for several approaches and yet no serious implementations and practical tools. In this thesis we address the aforementioned issues in a broad sense. We identify the preferential approach, by Kraus, Lehmann and Magidor (KLM) in propositional logic, as a suitable abstract framework for de ning and studying the precepts of sensible defeasible reasoning. We give a generalisation of KLM's precepts, and their arguments motivating them, to the DL case. We also provide several preferential algorithms for defeasible entailment in DLs; evaluate these algorithms, and the main alternatives in the literature, against the agreed upon precepts; extensively test the performance of these algorithms; and ultimately consolidate our implementation in a software tool called Defeasible-Inference Platform (DIP). We found some useful entailment regimes within the preferential context that satisfy all the KLM properties, and some that have scalable performance in real world ontologies even without extensive optimisation

Truth maintenance in knowledge-based systems

Truth Maintenance Systems (TMS) have been applied in a wide range of domains, from diagnosing electric circuits to belief revision in agent systems. There also has been work on using the TMS in modern Knowledge-Based Systems such as intelligent agents and ontologies. This thesis investigates the applications of TMSs in such systems. For intelligent agents, we use a “light-weight” TMS to support query caching in agent programs. The TMS keeps track of the dependencies between a query and the facts used to derive it so that when the agent updates its database, only affected queries are invalidated and removed from the cache. The TMS employed here is “light-weight” as it does not maintain all intermediate reasoning results. Therefore, it is able to reduce memory consumption and to improve performance in a dynamic setting such as in multi-agent systems. For ontologies, this work extends the Assumption-based Truth Maintenance System (ATMS) to tackle the problem of axiom pinpointing and debugging in ontology-based systems with different levels of expressivity. Starting with finding all errors in auto-generated ontology mappings using a “classic” ATMS [23], we extend the ATMS to solve the axiom pinpointing problem in Description Logics-based Ontologies. We also attempt this approach to solve the axiom pinpointing problem in a more expressive upper ontology, SUMO, whose underlying logic is undecidable