Jeremy Rogers

OWL Pizzas: Practical Experience of Teaching OWL-DL: Common Errors & Common Patterns

Understanding the logical meaning of any description logic or similar formalism is difficult for most people, and OWL-DL is no exception. This paper presents the most common difficulties encountered by newcomers to the language, that have been observed during the course of more than a dozen workshops, tutorials and modules about OWL-DL and it’s predecessor languages. It emphasises understanding the exact meaning of OWL expressions – proving that understanding by paraphrasing them in pedantic but explicit language. It addresses, specifically, the confusion which OWL’s open world assumption presents to users accustomed to closed world systems such as databases, logic programming and frame languages. Our experience has had a major influence in formulating the requirements for a new set of user interfaces for OWL the first of which are now available as prototypes. A summary of the guidelines and paraphrases and examples of the new interface are provided. The example ontologies are available online.

Ontological and Practical Issues in Using a Description Logic to Represent Medical Concept Systems: Experience from GALEN

GALEN seeks to provide re-usable terminology resources for clinical systems. The heart of GALEN is the Common Reference Model (CRM) formulated in a specialised description logic. The CRM is based on a set of principles that have evolved over the period of the project and illustrate key issues to be addressed by any large medical ontology. The principles on which the CRM is based are discussed followed by a more detailed look at the actual mechanisms employed. Finally the structure is compared with other biomedical ontologies in use or proposed.

The CLEF Chronicle: Patient Histories Derived from Electronic Health Records

Electronic patient records are typically optimised for delivering care to a single patient. They omit significant information that the care team can infer whilst including much of only transient value. They are secondarily an indelible legal record, comprised of heterogeneous documents reflecting local institutional processes as much as, or more than, the course of the patient’s illness. By contrast, the CLEF Chronicle is a unified, formal and parsimonious representation of how a patient’s illness and treatments unfold through time. Its primary goal is efficient querying of aggregated patient data for clinical research, but it also supports summarisation of individual patients and resolution of co-references amongst clinical documents. It is implemented as a semantic network compliant with a generic temporal object model whose specifics are derived from external sources of clinical knowledge organised around ontologies. We describe the reconstruction of patient chronicles from clinical records and the subsequent definition and execution of sophisticated clinical queries across populations of chronicles. We also outline how clinical simulations are used to test and refine the object model. Finally, we discuss a range of engineering and theoretical challenges raised by our work.

Syntactic-semantic tagging as a mediator between linguistic representations and formal models: an exercise in linking SNOMED to GALEN

Natural language understanding applications are good candidates to solve the knowledge acquisition bottleneck when designing large scale concept systems. However, a necessary condition is that systems are built that transform sentences into a meaning representation that is independent of the subtleties of linguistic structure that nevertheless underly the way language works. The Cassandra II syntactic-semantic tagging system fulfills this goal partially. Within the GALEN-IN-USE project, it is used to transform linguistic representations of surgical procedure expressions into conceptual representations. In this paper, the proctology chapter of the SNOMED V3.1 procedure axis was used as a testbed to evaluate the usefulness of this approach. A quantitative and qualitative analysis of the data obtained is presented, showing that the Cassandra system can indeed complement the manual modelling efforts being conducted in the GALEN-IN-USE project. The different requirements related to linguistic modelling versus conceptual modelling can partly be accounted for by using an interface ontology, of which the fine tuning will however remain an important effort.

An ontology driven collaborative development for biomedical terminologies: From the French CCAM to the Australian ICHI coding system

The CCAM French coding system of clinical procedures was developed between 1994 and 2004 using, in parallel, a traditional domain experts consensus method on one hand, and advanced methodologies of ontology driven semantic representation and multilingual generation on the other hand. These advanced methodologies were applied under the framework of an European Union collaborative research project named GALEN and produced a new generation of biomedical terminology. Following the interest in several countries and in WHO, the GALEN network has tested the application of the ontology driven tools to the existing reduced Australian ICHI coding system for interventions presently under investigation by WHO to check its ability and appropriateness to become the reference international coding system for procedures. The initial results are presented and discussed in terms of feasibility and quality assurance for sharing and maintaining consistent medical knowledge and allowing diversity in linguistic expressiveness of end users.

The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data

A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high-level anatomical terms to describe sample origin. First-pass annotation in high-throughput assays (e.g. large-scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies.

Modelling and reclassification of surgical procedures - experiences from the use of GALEN methods in the domain of thoracic surgery

This paper reports on experiences fromthe evaluation of GALEN methods for mapping of follow-up categories in the domain of thoracic surgery to an existing classification of surgical procedures. The mapping of the aggregated levels or groups of thoracic procedures presents a genuine problem in relation to strict hierarchical classifications, since the follow-up categories do not necessarily fit in the pre-set structure of the classification. Experiences from modelling of the traditional classification and of the follow-up categories are reported, and an analysis of the results is presented along with a discussion of opportunities and potential problems and pitfalls when applying GALEN models and tools.

The SOFG anatomy entry list (SAEL): an annotation tool for functional genomics data: Conference Papers - Report of a workshop on integration of anatomy ontologies, held at the MRC human genetics unit, Edinburgh, 7–8 April 2004

This conference brought the microbial genomics community together to share their most up-to-the-minute achievements, so much so that several talks cannot be covered here, as the work discussed has not yet been published. This meeting report has details of a cross-section of the talks from the sessions on ‘Genome analysis and comparative genomics’, ‘Computational genomics’ and ‘Functional genomics’, ranging from studies on complex environmental samples, to specific pathogenic bacteria, to yeasts. Copyright