Medical knowledge reengineering – converting major portions of the UMLS into a terminological knowledge base

Abstract We describe a semi-automatic knowledge engineering approach for converting the human anatomy and pathology portion of the UMLS metathesaurus into a terminological knowledge base. Particular attention is paid to the proper representation of part-whole hierarchies, which complement taxonomic ones as a major hierarchy-forming principle for anatomical knowledge. Our approach consists of four steps. First, concept definitions are automatically generated from the metathesaurus, with LOOM as the target language. Second, integrity checking of the emerging taxonomic and partonomic hierarchies is automatically carried out by the terminological classifier. Third, terminological cycles and inconsistencies are manually eliminated and, in the last step, the knowledge base built this way is incrementally refined by a medical expert. Our experiments were run on a terminological knowledge base which is composed of 164 000 concepts and 76 000 relations. Empirical evidence for the lack of logical consistency, adequacy and improper granularity of the UMLS knowledge source is given, and finally, assessments of what kind of efforts are needed to render the formal target representation structures complete and empirically adequate

Alignment of the UMLS semantic network with BioTop: Methodology and assessment

Motivation: For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using OWL DL as a formal representation language, which has become standard in the semantic Web. In order to make logic-based reasoning available for the resources annotated or categorized with the SN, a mapping ontology was developed aligning the SN with BioTop. Methods: The theoretical foundations and the practical realization of the alignment are being described, with a focus on the design decisions taken, the problems encountered and the adaptations of BioTop that became necessary. For evaluation purposes, UMLS concept pairs obtained from MEDLINE abstracts by a named entity recognition system were tested for possible semantic relationships. Furthermore, all semantic-type combinations that occur in the UMLS Metathesaurus were checked for satisfiability. Results: The effort-intensive alignment process required major design changes and enhancements of BioTop and brought up s

Strengths and Limitations of Formal Ontologies in the Biomedical Domain

We propose a typology of representational artifacts for health care and life sciences domains and associate this typology with different kinds of formal ontology and logic, drawing conclusions as to the strengths and limitations for ontology in a description logics framework. The four types of domain representation we consider are: (i) lexico-semantic representation, (ii) representation of types of entities, (iii) representations of background knowledge, and (iv) representation of individuals. We advocate a clear distinction of the four kinds of representation in order to provide a more rational basis for using ontologies and related artifacts to advance integration of data and enhance interoperability of associated reasoning systems. We highlight the fact that only a minor portion of scientifically relevant facts in a domain such as biomedicine can be adequately represented by formal ontologies as long as the latter are conceived as representations of entity types. In particular, the attempt to encode default or probabilistic knowledge using ontologies so conceived is prone to produce unintended, erroneous models

Vantagens e limitações das ontologias formais na área biomédica

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos

DCC Digital Curation Manual: Instalment on Ontologies

Instalment on the role of ontologies within the digital curation life-cycle. Describes the increasingly important role of ontologies for digital curation, some practical applications, the topic’s place within the OAIS reference model, and advice on developing institution-specific selection frameworks

Unintended consequences of existential quantifications in biomedical ontologies

<p>Abstract</p> <p>Background</p> <p>The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.</p> <p>Results</p> <p>We analyzed ontologies and ontology cross products available via the OBO Foundry site <url>http://www.obofoundry.org</url> for existential restrictions (<it>someValuesFrom</it>), from which we examined a random sample of 2,836 clauses.</p> <p>According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' <it>κ </it>= 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (<it>κ </it>= 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.</p> <p>Conclusions</p> <p>The current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.</p

A semantic-driven framework for IT support of clinical laboratory standards

The clinical laboratory plays a critical role in the delivery of care within the healthcare system by providing services that support accurate and timely diagnosis of diseases. The clinical laboratory relies on standard operating procedures (SOP) to provide information and guidance on the laboratory procedures. To ensure an excellent standard of clinical laboratory services, SOPs need to be of high quality, and practitioners need to have easy access to information contained within the SOPs. However, we argue in this thesis that there is a lack of standardization within clinical laboratory SOPs, and machines and human practitioners have difficulties accessing or using the content of SOPs. This thesis proposes a solution to challenges regarding the representation and use of SOPs in clinical laboratories (see Chapter 1). The research work in this thesis is based on the most up-to-date technological, theoretical, and empirical approaches (see Chapter 2). Additionally, external researchers have already utilized the outcome of this research for various purposes (see Chapter 5). In this thesis, we present the SmartSOP framework, a semantic-driven framework, that supports the representation of clinical laboratory procedure concepts in a standardised format for use within software applications. The SmartSOP framework consists of three main components, the Ontology for Clinical Laboratory SOP (OCL-SOP), the translation engine that converts free text SOPs to a standardised format, and a mobile application to provide lab practitioners with easy access to SOPs (see Chapters 3 and 4). We used the design science approach for the execution of this research work

Semantic Interoperability in Digital Library Systems

This report is a state-of-the-art overview of activities and research being undertaken in areas relating to semantic interoperability in digital library systems. It has been undertaken as part of the cluster activity of WP5: Knowledge Extraction and Semantic Interoperability (KESI). The authors and contributors draw on the research expertise and experience of a number of organisations (UKOLN, ICS-FORTH, NETLAB, TUC-MUSIC, University of Glamorgan) as well as several work-packages (WP5: Knowledge Extraction and Semantic Interoperability; WP3: Audio-Visual and Non-traditional Objects) within the DELOS2 NoE. In addition, a workshop was held [KESI Workshop Sept. 2004] (co-located with ECDL 2004) in order to provide a forum for the discussion of issues relevant to the topic of this report. We are grateful to those who participated in the forum and for their valuable comments, which have helped to shape this report. Definitions of interoperability, syntactic interoperability and semantic interoperability are presented noting that semantic interoperability is very much about matching concepts as a basis. The NSF Post Digital Libraries Futures Workshop: Wave of the Future [NSF Workshop] has identified semantic interoperability as being of primary importance in digital library research

Deploying ontologies in software design

In this thesis we will be concerned with the relation between ontologies and software design. Ontologies are studied in the artificial intelligence community as a means to explicitly represent standardised domain knowledge in order to enable knowledge shar¬ ing and reuse. We deploy ontologies in software design with emphasis on a traditional software engineering theme: error detection. In particular, we identify a type of error that is often difficult to detect: conceptual errors. These are related to the description of the domain whom which the system will operate. They require subjective knowledge about correct forms of domain description to detect them. Ontologies provide these forms of domain description and we are interested in applying them and verify their correctness(chapter 1). After presenting an in depth analysis of the field of ontologies and software testing as conceived and implemented by the software engineering and artificial intelligence communities(chapter 2), we discuss an approach which enabled us to deploy ontologies in the early phases of software development (i.e., specifications) in order to detect conceptual errors (chapter 3). This is based on the provision of ontological axioms which are used to verify conformance of specification constructs to the underpinning ontology. To facilitate the integration of ontology with applications that adopt it we developed an architecture and built tools to implement this form of conceptual error check(chapter 4). We apply and evaluate the architecture in a variety of contexts to identify potential uses (chapter 5). An implication of this method for de¬ ploying ontologies to reason about the correctness of applications is to raise our trust in the given ontologies. However, when the ontologies themselves are erroneous we might fail to reveal pernicious discrepancies. To cope with this problem we extended the architecture to a multi-layer form(chapter 4) which gives us the ability to check the ontologies themselves for correctness. We apply this multi-layer architecture to cap¬ ture errors found in a complex ontologies lattice(chapter 6). We further elaborate on the weaknesses in ontology evaluation methods and employ a technique stemming from software engineering, that of experience management, to facilitate ontology testing and deployment(chapter 7). The work presented in this thesis aims to improve practice in ontology use and identify areas to which ontologies could be of benefits other than the advocated ones of knowledge sharing and reuse(chapter 8)