Abstract: The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally it was assumed by many that this issue could be addressed simply by insisting on the... more
Abstract: The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally it was assumed by many that this issue could be addressed simply by insisting on the application of shared clinical terminologies. More recently however the use of the term 'ontology'has been steadily growing. We here address the issue of the degree to which the use of ontologies represents any real advance on the road to semantic interoperability. Keywords: Clinical Ontologies, Knowledge ...
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Research Interests: Image Processing, Medical Image Processing, Cell Cycle, Cellular Automata, Biomedical informatics, and 15 moreFinite Element, Stem Cell, Medical Imaging Informatics, Lung Cancer, Clinical Practice, Medical Image Segmentation, Medical Image Registration, Clinical Data, Clinical Study, Image Based Modelling, Differential equation, In Silico, Treatment Response, Cell Survival, and Imaging Informatics
In any realworld application scenario, natural language gen-eration (NLG) systems have to employ grammars consisting of tremendous amounts of rules. Detecting and fixing errors in such grammars is therefore a highly tedious task. In this... more
In any realworld application scenario, natural language gen-eration (NLG) systems have to employ grammars consisting of tremendous amounts of rules. Detecting and fixing errors in such grammars is therefore a highly tedious task. In this work we present a data mining ...
Quality assurance and audit issues play a major role in maintening large biomedical terminology, such as SNOMED CT. Several automatized techniques have been proposed to facilitate the identification of weak spots and suggest adequate... more
Quality assurance and audit issues play a major role in maintening large biomedical terminology, such as SNOMED CT. Several automatized techniques have been proposed to facilitate the identification of weak spots and suggest adequate improvements.In this study, we address a well-known issue within SNOMED CT: Albeit the wording of many free-text concept descriptions suggests a connection to other concepts, they are often not referred to in the logical concept definition.To detect such inconsistencies, we use a semantic indexing approach which maps free text onto a sequence of semantic identifiers. Applied to SNOMED CT concepts without attributes, our technique spots refinable concepts and suggests appropriate attributes, i.e., connections to other concepts. Based on a manual analysis of random samples, we estimate that approximately 18,000 refinable concepts can be found.
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ICBO: International Conference on Biomedical Ontology July 24-26, 2009▪ Buffalo, New York, USA Towards an Ontology of Biomedical Educational Objectives Martin Boeker, Holger Stenzhorn, Felix Balzer, Stefan Schulz Freiburg University... more
ICBO: International Conference on Biomedical Ontology July 24-26, 2009▪ Buffalo, New York, USA Towards an Ontology of Biomedical Educational Objectives Martin Boeker, Holger Stenzhorn, Felix Balzer, Stefan Schulz Freiburg University Medical Center, Freiburg i. Br., ...
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Zusammenfassung: In der biomedizinischen Forschung werden besonders in den letzten Jahren vermehrt enorme Mengen an neuen Daten produziert und diese in Folge verstärkt per Internet veröffentlicht. Viele Experten sehen in dieser... more
Zusammenfassung: In der biomedizinischen Forschung werden besonders in den letzten Jahren vermehrt enorme Mengen an neuen Daten produziert und diese in Folge verstärkt per Internet veröffentlicht. Viele Experten sehen in dieser Vorge-hensweise die Chance zur ...
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In this paper we present XtraGen, a XML-and Java-based software system for the flexible, real-time generation of natural language that is easily inte-grated and used in real-world applications. We de-scribe its grammar formalism and... more
In this paper we present XtraGen, a XML-and Java-based software system for the flexible, real-time generation of natural language that is easily inte-grated and used in real-world applications. We de-scribe its grammar formalism and implementation in detail, depict ...
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Clinical documentation needs to be fine-grained to truthfully represent the history, development, and treatment of a patient. But natural language, as the main inform ation carrier, is characterized by many issues, like idiosyncratic... more
Clinical documentation needs to be fine-grained to truthfully represent the history, development, and treatment of a patient. But natural language, as the main inform ation carrier, is characterized by many issues, like idiosyncratic terminology, spelling and grammar errors, and a l ack of gra mmatical structure. Therefore coding systems, like ICD-10, have been introduced, but their use varies highly among
Research Interests: Information Retrieval, Medical Informatics, Natural Language Processing, Documentation, Knowledge Representation, and 8 moreLibrary and Information Studies, Natural language, SNOMED CT, Description Logic, Public health systems and services research, Exponential Growth, Electronic Medical Record, and Automatic data processing
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Abstract: The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally it was assumed by many that this issue could be addressed simply by insisting on the... more
Abstract: The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally it was assumed by many that this issue could be addressed simply by insisting on the application of shared clinical terminologies. More recently however the use of the term 'ontology'has been steadily growing. We here address the issue of the degree to which the use of ontologies represents any real advance on the road to semantic interoperability.
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The challenge of modelling cancer presents a major opportunity to improve our ability to reduce mortality from malignant neoplasms, improve treatments and meet the demands associated with the individualization of care needs. This is the... more
The challenge of modelling cancer presents a major opportunity to improve our ability to reduce mortality from malignant neoplasms, improve treatments and meet the demands associated with the individualization of care needs. This is the central motivation behind the ContraCancrum project. By developing integrated multi-scale cancer models, ContraCancrum is expected to contribute to the advancement of in silico oncology through the optimization of cancer treatment in the patient-individualized context by simulating the response to various therapeutic regimens. The aim of the present paper is to describe a novel paradigm for designing clinically driven multi-scale cancer modelling by bringing together basic science and information technology modules. In addition, the integration of the multi-scale tumour modelling components has led to novel concepts of personalized clinical decision support in the context of predictive oncology, as is also discussed in the paper. Since clinical adapt...
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We present an information system, which was developed within the project MIETTA (Multilingual Information Extraction for Tourism and Travel Assistance), a project in the Language Engineering Sector of the Telematics Application Program of... more
We present an information system, which was developed within the project MIETTA (Multilingual Information Extraction for Tourism and Travel Assistance), a project in the Language Engineering Sector of the Telematics Application Program of the European Commission. MIETTA facilitates multilingual information access in a number of languages (English, Finnish, French, German, Italian) to the tourist information (web documents and database information)
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Clinical Trial Management Systems promise to help researchers in managing the large amounts of data occurring in clinical trials. In such systems Case Report Forms for capturing all patient data can usually be defined freely for a given... more
Clinical Trial Management Systems promise to help researchers in managing the large amounts of data occurring in clinical trials. In such systems Case Report Forms for capturing all patient data can usually be defined freely for a given trial. But if database definitions are automatically derived from such trial-specific definitions then the collected data cannot be easily compared to or integrated into other trials. We address this interoperability issue with an approach based on ontology and semantic data mediation. This resulted in the development of the ObTiMA system which is composed of a component for setting-up clinical trials and another for handling patient data during trials. Both components offer data reusability by relying on shared concepts defined in an ontology covering the whole cancer care and research spectrum.
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Semantic interoperability is a major desideratum in health care for computer-based documentation and communication through electronic health records. They require structured data ideally represented via standardized information models,... more
Semantic interoperability is a major desideratum in health care for computer-based documentation and communication through electronic health records. They require structured data ideally represented via standardized information models, e.g., HL7 RIM or openEHR, connected to standardized terminologies or ontologies, e.g., SNOMED CT or LOINC. But since natural language is seen by health professionals as their most natural and effective form
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Classifying biological entities in terms of species and taxa is an important endeavor in biology. But even though many statements within current biomedical ontologies are indeed taxon-dependent, no standard way exists to properly... more
Classifying biological entities in terms of species and taxa is an important endeavor in biology. But even though many statements within current biomedical ontologies are indeed taxon-dependent, no standard way exists to properly introduce taxon or species information into current ontological architectures. Therefore we discuss various practices to represent such information by applying a biomedical top-level ontology combined with other standard approaches like description logics or the OBO Foundry.
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We present ten principles for clinical ontologies that describe the authors' opinion about what should be understood by the notion of clinical ontologies and what not. In contrast to clinical terminology systems, clinical ontologies... more
We present ten principles for clinical ontologies that describe the authors' opinion about what should be understood by the notion of clinical ontologies and what not. In contrast to clinical terminology systems, clinical ontologies are considered to be semantic reference systems and for that--first of all--strive to account for the properties of the domain entities themselves and their proper formal definitions--rather than just linking clinical terms together.
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In this paper we present the ongoing development and extension work on BioTop--a top-domain ontology for linking biomedical domain ontologies. We start by making the case for the application of a common ontology to interface independent... more
In this paper we present the ongoing development and extension work on BioTop--a top-domain ontology for linking biomedical domain ontologies. We start by making the case for the application of a common ontology to interface independent biomedical domain ontologies by introducing a set of more general classes. Then we briefly depict the relation of BioTop to the GENIA ontology as starting point of its initial developement. Afterwards we propose our distinction of ontologies into top, top-domain and domain ones and describe our approach to the integration of the top ontology BFO into BioTop. Then we present our plans to join the OBO and OBO Foundry repository of ontologies and list its admission principles in relation to our ontology. 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.
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The application of upper ontologies has been repeatedly advocated for supporting interoperability between domain ontologies in order to facilitate shared data use both within and across disciplines. We have developed BioTop as a... more
The application of upper ontologies has been repeatedly advocated for supporting interoperability between domain ontologies in order to facilitate shared data use both within and across disciplines. We have developed BioTop as a top-domain ontology to integrate more specialized ontologies in the biomolecular and biomedical domain. In this paper, we report on concrete integration problems of this ontology with the domain-independent Basic Formal Ontology (BFO) concerning the issue of fiat and aggregated objects in the context of different granularity levels. We conclude that the third BFO level must be ignored in order not to obviate cross-granularity integration.
Research Interests: Programming Languages, Formal Ontology, Systems Integration, Library and Information Studies, Humans, and 7 moreComputer User Interface Design, Information Storage and Retrieval, Ontology Integration, Domain Ontology, Public health systems and services research, Basic Formal Ontology, and Unified Medical Language System
The @neurIST ontology is currently under development within the scope of the European project @neurIST intended to serve as a module in a complex architecture aiming at providing a better understanding and management of intracranial... more
The @neurIST ontology is currently under development within the scope of the European project @neurIST intended to serve as a module in a complex architecture aiming at providing a better understanding and management of intracranial aneurysms and subarachnoid hemorrhages. Due to the integrative structure of the project the ontology needs to represent entities from various disciplines on a large spatial and temporal scale. Initial term acquisition was performed by exploiting a database scaffold, literature analysis and communications with domain experts. The ontology design is based on the DOLCE upper ontology and other existing domain ontologies were linked or partly included whenever appropriate (e.g., the FMA for anatomical entities and the UMLS for definitions and lexical information). About 2300 predominantly medical entities were represented but also a multitude of biomolecular, epidemiological, and hemodynamic entities. The usage of the ontology in the project comprises termin...
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Usability testing methods are nowadays integrated into the design and development of health-care software, and the need for usability in health-care information technology (IT) is widely accepted by clinicians and researchers. Usability... more
Usability testing methods are nowadays integrated into the design and development of health-care software, and the need for usability in health-care information technology (IT) is widely accepted by clinicians and researchers. Usability assessment starts with the identification of specific objectives that need to be tested and continues with the definition of evaluation criteria and monitoring procedures before usability tests are performed to assess the quality of all services and tasks. Such a process is implemented in the p-medicine environment and gives feedback iteratively to all software developers in the project. GCP (good clinical practice) criteria require additional usability testing of the software. For the p-medicine project (www.p-medicine.eu), an extended usability concept (EUC) was developed. The EUC covers topics like ease of use, likeability, and usefulness, usability in trial centres characterised by a mixed care and research environment and by extreme time constra...
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The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application... more
The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term 'ontology' has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects.
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Research Interests: Information Systems, Genetics, Medical Informatics, Genomics, Software, and 9 moreComputers, Library and Information Studies, Humans, Pharmacogenetics, Decision Support, Information Infrastructure, Public health systems and services research, Clinical Decision Support Systems, and Treatment Response
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Clinical documentation needs to be fine-grained to truthfully represent the history, development, and treatment of a patient. But natural language, as the main inform ation carrier, is characterized by many issues, like idiosyncratic... more
Clinical documentation needs to be fine-grained to truthfully represent the history, development, and treatment of a patient. But natural language, as the main inform ation carrier, is characterized by many issues, like idiosyncratic terminology, spelling and grammar errors, and a l ack of gra mmatical structure. Therefore coding systems, like ICD-10, have been introduced, but their use varies highly among
Research Interests: Information Retrieval, Medical Informatics, Natural Language Processing, Documentation, Knowledge Representation, and 8 moreLibrary and Information Studies, Natural language, SNOMED CT, Description Logic, Public health systems and services research, Exponential Growth, Electronic Medical Record, and Automatic data processing
In the life sciences, there is an ample need for semantic interoperability of d ata. Thus shared vocabularies are needed for consistently expressing meta data in terms of semantic annotations as well as for querying bibliographic... more
In the life sciences, there is an ample need for semantic interoperability of d ata. Thus shared vocabularies are needed for consistently expressing meta data in terms of semantic annotations as well as for querying bibliographic information systems. In the past years, lots of highly specialized, yet also fragmented terminolog ies have evolved. However, they lack principled forms of conceptual
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The application of upper ontologies has been repeatedly advocated for to support the interoperability between different domain ontologies for facilitating the shared use of data within and across disciplines. BioTop is an upper domain... more
The application of upper ontologies has been repeatedly advocated for to support the interoperability between different domain ontologies for facilitating the shared use of data within and across disciplines. 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. BFO was manually integrated into BioTop, observing both its free text and formal definitions. BioTop classes were attached to BFO classes as children and BFO classes were reused in the formal definitions of BioTop classes. A description logics reasoner was used to check the logical consistency of this integration. The domain adequacy was checked manually by domain experts. Logical inconsistencies were found by the reasoner when applying the BFO classes for fiat and aggregated objects in some of the BioTop class definitions. We discovered that the definition of those particular classes in BFO was dependent on the notion of physical connectedness. Hence we suggest ignoring a BFO subbranch in order not to hinder cross-granularity integration. Without introducing a more sophisticated theory of granularity, the described problems cannot be properly dealt with. Whereas we argue that an upper ontology should be granularity-independent, we illustrate how granularity-dependent domain ontologies can still be embedded into the framework of BioTop in combination with BFO.