Stefan Schulz

....

..We conclude that the third BFO level must be ignored in order not to obviate cross-granularity integration...

..There are two benefits in pursuing such an approach. First, it provides a foundation for logic-based CGP fusion and collision detection. Second, it allows for the checking of clinical treatment episodes from the EPR against CGPs...

..For the biomedical domain, it is not only crucial to cope with ontological dependencies between wholes and their parts but also with specific reasoning patterns which underlie the propagation of roles across partonomic hierarchies...

..We analyze these ambiguities and make suggestions for a standardization of mereological relations in biomedical ontologies...

..In this article, we analyze a special encoding scheme for diseases and procedures in SNOMED CT, the so-called relationship groups (RGs), which had been devised to avoid ambiguities in definitions...

..An adequate and expressive ontological representation of biological organisms and their parts requires formal reasoning mechanisms for their relations of physical aggregation and containment...

..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...

..BioTop is an upper domain ontology that aims at aligning more specialized biomolecular and biomedical ontologies. The integration of BioTop and the upper ontology Basic Formal Ontology (BFO) is the objective of this study...

....

..Support for the symbolic representation of the physical structure of living organisms by an ontologically solid and logically sound foundation as a basis for formal reasoning...

..We recommend that in a future revision of the ICD, compatibility with the then existing classification system should be considered...

....

..The number of full definitions should be increased. Finally, we propose a new approach to modeling part-whole hierarchies, as well as the integration of qualifier relations into the description logic framework...

..All proposed modifications can be expressed by the computationally tractable description logic EL(++)...

..We present a tool for thesaurus compilation and management, and outline a methodology for the proper construction and maintenance of a multilingual morpheme thesaurus...

..Acknowledging its merits as a standard reporting instrument for change management and process improvements we propose formal improvements...

..The second problem, cross-lingual medical document retrieval, is dealt with by defining cross-lingual equivalence relations on the emerging morpheme sets...

..SNOMED CT claims to support formal reasoning by description-logic based concept definitions...

....

..We present a method for the automated acquisition of a multilingual medical lexicon (for Spanish, French and Swedish) to be used within the framework of a medical cross-language text retrieval system...

..e. semantically minimal units. Using two different standard test collections for the medical domain, we evaluate our approach for six languages covered by our system...

..We provide a query example that indicates that ontological querying over heterogeneous information models is feasible via SPARQL construct- and resource mapping queries...

..We also present data for the information extraction performance of MEDSYNDIKATE in terms of the semantic interpretation of three major syntactic patterns in medical documents...

..Based on a series of retrieval experiments, we have gathered evidence that subword-based indexing and retrieval for the German biomedical sublanguage, at least--outperforms conventional string matching approaches...

..Based on these data we predict roughly 716 non-coded diabetes cases, 13 non-coded Parkinson cases, and 420 non-coded asthma/COPD cases among 34,865 treatment episodes...

..Based on this we implemented a prototypical system which incorporates both the OpenNLP and the MorphoSaurus natural language processing systems...

..We evaluate this approach using the OHSUMED corpus, a large medical document collection, within a cross-language retrieval setting...

..We propose an interlingua-based indexing approach to account for the particular challenges that arise in the design and implementation of cross-language document retrieval systems for the medical domain...

....

..The necessity to raise the quality level of electronic publications is stressed considering aspects of domain knowledge, software engineering, media development, interface design and didactics...

..Our suggestions are based on experience with MEDSYNDIKATE, a medical text knowledge acquisition system designed to properly deal with various sorts of discourse structure phenomena...

..These provide an adequate methodology for designing more sophisticated, flexible medical ontologies serving the needs of 'deep' knowledge applications which are by no means restricted to medical language processing...

..whereas in developing countries these media are scarce and expensive. Here CBT programs, and hypermedia publications in particular, may be a cost-effective way to improve quality of education in the health sector...

..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...

..The increasing amount of electronically available documents in bibliographic databases and the clinical documentation requires user-friendly techniques for content retrieval...

..After identifying typical error patterns we discuss some possible improvements. Our recommendation is to either amend the problematic axioms in the OWL-DL formalization or to consider some less strict representational format...

..We studied the quality of web sites containing information on gastrointestinal cancer, focusing on the way these web sites dealt with the special concerns of these patients...

..Considering the ongoing standardization of health terminologies and classifications, we strongly recommend to improve the ICHI structure, capitalizing on the benefits of the CCAM architecture...

..The requirements and the accompanying system architecture could be satisfactorily implemented...

..Access statistics are presented which demonstrate its relevance as well as the geographical focus of Health Informatics research and development...

..We describe the architecture and typical features of virtual conferences, their organizational and technical requirements and discuss prerequisites for their successful implementation...

..By using a specific experimental design, we are able to quantify the impact of cross-lingual information in coping with underspecification in formal ontologies...

..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 overall quality improvement of the thesaurus was finally measured using the OHSUMED IR benchmark, resulting in a significant improvement of the retrieval quality for one of the languages tested...

..Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH...

..The GRO has just been submitted to the OBO library and is currently under review. It is available at http://www.ebi.ac.uk/Rebholz-srv/GRO/GRO.html...

..We identify four types of such anomalies. We also analyzed to which extent the anomalous lexicon entries had been detected by an alternative, corpus-based approach...

..Some actual BioTop interface classes are shown subsequently. We conclude by detailing on some planned BioTop usages in the area of BioNLP and cancer research and show some further intended improvements...

..Feeding experiments with deuterated propionate showed that chortolure is a polyketide, formed by successive addition of four propionate units to an acetate starter...

....