In systems biology, networks represent components of biological systems and their interactions. I... more In systems biology, networks represent components of biological systems and their interactions. It is a challenge to efficiently represent, integrate and analyse the wealth of information that is now being created in biology, where issues concerning consistency arise. As well, the information offers novel methods to explain and explore biological phenomena.
Abstract Units are basic scientific tools that render meaning to numerical data. Their standardiz... more Abstract Units are basic scientific tools that render meaning to numerical data. Their standardization and formalization caters for the report, exchange, process, reproducibility and integration of quantitative measurements. Ontologies are means that facilitate the integration of data and knowledge allowing interoperability and semantic information processing between diverse biomedical resources and domains.
Despite considerable progress in understanding the molecular origins of hereditary human diseases... more Despite considerable progress in understanding the molecular origins of hereditary human diseases, the molecular basis of several thousand genetic diseases still remains unknown. High-throughput phenotype studies are underway to systematically assess the phenotype outcome of targeted mutations in model organisms. Thus, comparing the similarity between experimentally identified phenotypes and the phenotypes associated with human diseases can be used to suggest causal genes underlying a disease.
Abstract Motivation: The systematic observation of phenotypes has become a crucial tool of functi... more Abstract Motivation: The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed.
ABSTRACT As the amount of data being generated in biology has increased, a major challenge has be... more ABSTRACT As the amount of data being generated in biology has increased, a major challenge has been how to store and represent this data in a way that makes it easily accessible to researchers from diverse domains. Understanding the relationship between genotype and phenotype is a major focus of biological research. Various approaches to providing the link between genes and their functions have been undertaken–most require significant and dedicated manual curation.
ABSTRACT The field of drug discovery has experienced in the recent years a growth in the number o... more ABSTRACT The field of drug discovery has experienced in the recent years a growth in the number of computational methods used to predict new biological actions for chemical compounds. In order to evaluate predictions and to gain insights into the potential usage of drugs, the Anatomical Therapeutic Chemical Classification System (ATC) serves as an internationally accepted gold standard.
ABSTRACT The biological meaning of physics-based simulations of biological processes is usually i... more ABSTRACT The biological meaning of physics-based simulations of biological processes is usually implicit, and often inaccessible to biological researchers, or indeed to any researchers beyond the authors of a particular model. To display and interrogate the physiological content of such models, we have developed formal semantic models of biological process networks that we call PhysioMaps.
Abstract. Realist ontologies claim to represent what exists. Scientific discourse, however, often... more Abstract. Realist ontologies claim to represent what exists. Scientific discourse, however, often contains terms of dubious reference when describing current or past hypotheses, plans, or ideas. We present a framework in which a realist ontology is embedded in a description logics theory, the latter being indifferent regarding the existence of class members. It therefore may include units for various kinds of such terms.
Abstract: Applied ontology is a relatively new field which aims to apply theories and methods fro... more Abstract: Applied ontology is a relatively new field which aims to apply theories and methods from diverse disciplines such as philosophy, cognitive science, linguistics and formal logics to perform or improve domain-specific tasks. To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated.
In systems biology, networks represent components of biological systems and their interactions. I... more In systems biology, networks represent components of biological systems and their interactions. It is a challenge to efficiently represent, integrate and analyse the wealth of information that is now being created in biology, where issues concerning consistency arise. As well, the information offers novel methods to explain and explore biological phenomena.
Abstract Units are basic scientific tools that render meaning to numerical data. Their standardiz... more Abstract Units are basic scientific tools that render meaning to numerical data. Their standardization and formalization caters for the report, exchange, process, reproducibility and integration of quantitative measurements. Ontologies are means that facilitate the integration of data and knowledge allowing interoperability and semantic information processing between diverse biomedical resources and domains.
Despite considerable progress in understanding the molecular origins of hereditary human diseases... more Despite considerable progress in understanding the molecular origins of hereditary human diseases, the molecular basis of several thousand genetic diseases still remains unknown. High-throughput phenotype studies are underway to systematically assess the phenotype outcome of targeted mutations in model organisms. Thus, comparing the similarity between experimentally identified phenotypes and the phenotypes associated with human diseases can be used to suggest causal genes underlying a disease.
Abstract Motivation: The systematic observation of phenotypes has become a crucial tool of functi... more Abstract Motivation: The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed.
ABSTRACT As the amount of data being generated in biology has increased, a major challenge has be... more ABSTRACT As the amount of data being generated in biology has increased, a major challenge has been how to store and represent this data in a way that makes it easily accessible to researchers from diverse domains. Understanding the relationship between genotype and phenotype is a major focus of biological research. Various approaches to providing the link between genes and their functions have been undertaken–most require significant and dedicated manual curation.
ABSTRACT The field of drug discovery has experienced in the recent years a growth in the number o... more ABSTRACT The field of drug discovery has experienced in the recent years a growth in the number of computational methods used to predict new biological actions for chemical compounds. In order to evaluate predictions and to gain insights into the potential usage of drugs, the Anatomical Therapeutic Chemical Classification System (ATC) serves as an internationally accepted gold standard.
ABSTRACT The biological meaning of physics-based simulations of biological processes is usually i... more ABSTRACT The biological meaning of physics-based simulations of biological processes is usually implicit, and often inaccessible to biological researchers, or indeed to any researchers beyond the authors of a particular model. To display and interrogate the physiological content of such models, we have developed formal semantic models of biological process networks that we call PhysioMaps.
Abstract. Realist ontologies claim to represent what exists. Scientific discourse, however, often... more Abstract. Realist ontologies claim to represent what exists. Scientific discourse, however, often contains terms of dubious reference when describing current or past hypotheses, plans, or ideas. We present a framework in which a realist ontology is embedded in a description logics theory, the latter being indifferent regarding the existence of class members. It therefore may include units for various kinds of such terms.
Abstract: Applied ontology is a relatively new field which aims to apply theories and methods fro... more Abstract: Applied ontology is a relatively new field which aims to apply theories and methods from diverse disciplines such as philosophy, cognitive science, linguistics and formal logics to perform or improve domain-specific tasks. To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated.
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