Towards Improving Phenotype Representation in OWL

BACKGROUND: Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. METHODS: We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. RESULTS: In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. CONCLUSION: Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions

OBML - Ontologies in Biomedicine and Life Sciences

The OBML 2010 workshop, held at the University of Mannheim on September 9-10, 2010, is the 2(nd) in a series of meetings organized by the Working Group “Ontologies in Biomedicine and Life Sciences” of the German Society of Computer Science (GI) and the German Society of Medical Informatics, Biometry and Epidemiology (GMDS). Integrating, processing and applying the rapidly expanding information generated in the life sciences — from public health to clinical care and molecular biology — is one of the most challenging problems that research in these fields is facing today. As the amounts of experimental data, clinical information and scientific knowledge increase, there is a growing need to promote interoperability of these resources, support formal analyses, and to pre-process knowledge for further use in problem solving and hypothesis formulation. The OBML workshop series pursues the aim of gathering scientists who research topics related to life science ontologies, to exchange ideas, discuss new results and establish relationships. The OBML group promotes the collaboration between ontologists, computer scientists, bio-informaticians and applied logicians, as well as the cooperation with physicians, biologists, biochemists and biometricians, and supports the establishment of this new discipline in research and teaching. Research topics of OBML 2010 included medical informatics, Semantic Web applications, formal ontology, bio-ontologies, knowledge representation as well as the wide range of applications of biomedical ontologies to science and medicine. A total of 14 papers were presented, and from these we selected four manuscripts for inclusion in this special issue. An interdisciplinary audience from all areas related to biomedical ontologies attended OBML 2010. In the future, OBML will continue as an annual meeting that aims to bridge the gap between theory and application of ontologies in the life sciences. The next event emphasizes the special topic of the ontology of phenotypes, in Berlin, Germany on October 6-7, 2011

A UML Profile for Functional Modeling Applied to the Molecular Function Ontology

ABSTRACT Gene Ontology (GO) is the largest, and steadily growing, resource for cataloging gene products. Naturally, its growth raises issues regarding its structure. Modeling and refactoring big ontologies such as GO is far from being simple. It seems that human-friendly graphical modeling languages, such as the Unified Modeling Language (UML) could be helpful for that task. In the current paper we investigate if UML can be utilized for making the structural organization of the Molecular Function Ontology (MFO), a sub-ontology of GO, more explicit. In addition, we examine if and how using UML can support the refactoring of MFO. We utilize UML and its extension mechanism for the definition of a UML dialect, which is suited for modeling functions and is called Function Modeling Language (FuML). Next, we use FuML for capturing the structure of molecular functions. Finally, we propose and demonstrate some refactoring options for MFO

A platform for collaborative management of semantic grid metadata

Grid environments, providing distributed infrastructures, computing resources and data storage, usually show a high degree of heterogeneity in their metadata. We propose a platform for collaborative management and maintenance of common metadata for grids. As the conceptual foundation of this platform, a meta model is presented which distinguishes structured descriptions and classification structures. On this basis, the system allows for the user-friendly creation and editing of grid relevant metadata and provides various search and navigation facilities for grid participants. We applied the platform to the German D-Grid initiative by establishing the D-Grid Ontology (DGO)

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.

MOTIVATION: Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. RESULTS: We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. AVAILABILITY: The BOWiki and supplementary material is available at . The source code is available under the GNU GPL from

Ontological Semantics: An Attempt at Foundations of Ontology Representation

The original and still a major purpose of ontologies in computer and information sciences is to serve for the semantic integration of represented content, facilitating information system interoperability. Content can be data, information, and knowledge, and it can be distributed within or across these categories. A myriad of languages is available for representation. Ontologies themselves are artifacts which are expressed in various languages. Different such languages are utilized today, including, as well-known representatives, predicate logic, subsuming first-order (predicate) logic (FOL), in particular, and higher-order (predicate) logic (HOL); the Web Ontology Language (OWL) on the basis of description logics (DL); and the Unified Modeling Language (UML). We focus primarily on languages with formally defined syntax and semantics. This overall picture immediately suggests questions of the following kinds: What is the relationship between an ontology and the language in which it is formalized? Especially, what is the impact of the formal semantics of the language on the formalized ontology? How well understood is the role of ontologies in semantic integration? Can the same ontology be represented in multiple languages and/or in distinct ways within one language? Is there an adequate understanding of whether two expressions are intensionally/conceptually equivalent and whether two ontologies furnish the same ontological commitments? One may assume that these questions are resolved. Indeed, the development and adoption of ontologies is widespread today. Ontologies are authored in a broad range of different languages, including offering equally named ontologies in distinct languages. Much research is devoted to techniques and technologies that orbit ontologies, for example, ontology matching, modularization, learning, and evolution, to name a few. Ontologies have found numerous beneficial applications, and hundreds of ontologies have been created, considering solely the context of biomedical research. For us, these observations increase the relevance of the stated questions and close relatives thereof, and raise the desire for solid theoretical underpinnings. In the literature of computer and information sciences, we have found only few approaches that tackle the foundations of ontologies and their representation to allow for answering such questions or that actually answer them. We elaborate an analysis of the subject as the first item of central contributions within this thesis. It mainly results in the identification of a vicious circularity in (i) the intended use of ontologies to mediate between formal representations and (ii) solely exploiting formal semantic notions in representing ontologies and defining ontology-based equivalence as a form of intensional/conceptual equivalence. On this basis and in order to overcome its identified limitations, we contribute a general model-theoretic semantic account, named \\\"ontological semantics\\\". This kind of semantics takes the approach of assigning arbitrary entities as referents of atomic symbols and to link syntactic constructions with corresponding ontological claims and commitments. In particular, ontological semantics targets the avoidance of encoding effects in its definition. Therefore we argue that this semantic account is well suited for interpreting formalized ontologies and for defining languages for the representation of ontologies. It is further proposed as a fundament for envisioned novel definitions of the intensional equivalence of expressions, in potential deviation from only being formally equivalent under set-theoretic semantics. The thesis is defended that a particular usage of a formalism and its respective vocabulary should be accompanied by establishing an ontological semantics that is tailored to that use of the formalism, in parallel to the formal semantics of the language, in order to capture the ontological content of the formal representation for adequate reuse in other formalisms. Accordingly, we advocate ontological semantics as a useful framework for justifying translations on an intensional basis. Despite all deviations of ontological semantics from its set-theoretic blueprint, close relationships between the two can be shown, which allow for using established FOL and DL reasoners while assuming ontological semantics.:* Preface ** Abstract ** Contents ** Acknowledgments ** Foreword 1 Introduction 1.1 Background 1.2 Motivations 1.3 Theses, Objectives and Scope 1.4 Outline and Contributions 1.5 Formal Preliminaries 2 Foundations on Languages, Semantics, and Ontology 2.1 Formal Syntax and Formal Semantics 2.2 The Role of Ontologies in Semantic Integration 2.3 Ontological Analysis and Meta-Ontological Architecture 2.4 Conceptualization of Categories and Relations - CR 2.5 Summary of the Analysis and Next Steps 3 Views on Set-Theoretic Semantics of Classical Predicate Logics 3.1 Tarskian Model Theory and Set-Theoretic Superstructure 3.2 Formal Semantics and Choices for Entity Postulation 3.3 Theory View of Semantics 3.4 Aims for an Ontologically Neutral Semantic Account 4 Ontological Semantics 4.1 Definition of Ontological Structures by Analogy to the Set-Theoretic Approach 4.2 Properties and Further Background for Ontological Structures in General 4.3 Ontological Models & Signature Aspects 4.4 Semantics of Predication 4.5 Semantics of Connectives and Quantifiers & Semantic Notions 4.6 Relations between Ontological and Set-Theoretic Semantics 4.7 Ontological Neutrality 5 Ontological Engineering and Applications 5.1 Formalization Method for Ontology Representation in FOL 5.2 Ontological Usage Schemes 5.3 Glimpse on Characterizing Modular Representation 5.4 Applications in the Biomedical Domain 6 Contributions to Ontologies 6.1 Formalizations of Categories and Relations - CR 6.2 Remarks on Further Contributions 6.3 Ontologies of Time 7 Conclusion and Continuation 7.1 Resume 7.2 Related Work 7.3 Conclusions 7.4 Beginnings of Future Work Appendix A Additional Preliminaries A.1 Logical Notions A.2 Axiomatic Systems of Set and Number Theory B Axioms of the CR Taxonomy in OWL B.1 Asserted OWL Class Axioms B.2 Asserted OWL Object Property Axioms C Lists of Figures and Tables C.1 List of Figures C.2 List of Tables D Abbreviations, Acronyms and Names D.1 Abbreviations D.2 Acronyms and Names E References E.1 Literature References E.2 Web References/List of URLs F Work and Author Information ** Selbständigkeitserklärung (Declaration of Authorship) ** Bibliographic Data ** Scientific Recor

Ontological Semantics: An Attempt at Foundations of Ontology Representation

The original and still a major purpose of ontologies in computer and information sciences is to serve for the semantic integration of represented content, facilitating information system interoperability. Content can be data, information, and knowledge, and it can be distributed within or across these categories. A myriad of languages is available for representation. Ontologies themselves are artifacts which are expressed in various languages. Different such languages are utilized today, including, as well-known representatives, predicate logic, subsuming first-order (predicate) logic (FOL), in particular, and higher-order (predicate) logic (HOL); the Web Ontology Language (OWL) on the basis of description logics (DL); and the Unified Modeling Language (UML). We focus primarily on languages with formally defined syntax and semantics. This overall picture immediately suggests questions of the following kinds: What is the relationship between an ontology and the language in which it is formalized? Especially, what is the impact of the formal semantics of the language on the formalized ontology? How well understood is the role of ontologies in semantic integration? Can the same ontology be represented in multiple languages and/or in distinct ways within one language? Is there an adequate understanding of whether two expressions are intensionally/conceptually equivalent and whether two ontologies furnish the same ontological commitments? One may assume that these questions are resolved. Indeed, the development and adoption of ontologies is widespread today. Ontologies are authored in a broad range of different languages, including offering equally named ontologies in distinct languages. Much research is devoted to techniques and technologies that orbit ontologies, for example, ontology matching, modularization, learning, and evolution, to name a few. Ontologies have found numerous beneficial applications, and hundreds of ontologies have been created, considering solely the context of biomedical research. For us, these observations increase the relevance of the stated questions and close relatives thereof, and raise the desire for solid theoretical underpinnings. In the literature of computer and information sciences, we have found only few approaches that tackle the foundations of ontologies and their representation to allow for answering such questions or that actually answer them. We elaborate an analysis of the subject as the first item of central contributions within this thesis. It mainly results in the identification of a vicious circularity in (i) the intended use of ontologies to mediate between formal representations and (ii) solely exploiting formal semantic notions in representing ontologies and defining ontology-based equivalence as a form of intensional/conceptual equivalence. On this basis and in order to overcome its identified limitations, we contribute a general model-theoretic semantic account, named \\\"ontological semantics\\\". This kind of semantics takes the approach of assigning arbitrary entities as referents of atomic symbols and to link syntactic constructions with corresponding ontological claims and commitments. In particular, ontological semantics targets the avoidance of encoding effects in its definition. Therefore we argue that this semantic account is well suited for interpreting formalized ontologies and for defining languages for the representation of ontologies. It is further proposed as a fundament for envisioned novel definitions of the intensional equivalence of expressions, in potential deviation from only being formally equivalent under set-theoretic semantics. The thesis is defended that a particular usage of a formalism and its respective vocabulary should be accompanied by establishing an ontological semantics that is tailored to that use of the formalism, in parallel to the formal semantics of the language, in order to capture the ontological content of the formal representation for adequate reuse in other formalisms. Accordingly, we advocate ontological semantics as a useful framework for justifying translations on an intensional basis. Despite all deviations of ontological semantics from its set-theoretic blueprint, close relationships between the two can be shown, which allow for using established FOL and DL reasoners while assuming ontological semantics.:* Preface ** Abstract ** Contents ** Acknowledgments ** Foreword 1 Introduction 1.1 Background 1.2 Motivations 1.3 Theses, Objectives and Scope 1.4 Outline and Contributions 1.5 Formal Preliminaries 2 Foundations on Languages, Semantics, and Ontology 2.1 Formal Syntax and Formal Semantics 2.2 The Role of Ontologies in Semantic Integration 2.3 Ontological Analysis and Meta-Ontological Architecture 2.4 Conceptualization of Categories and Relations - CR 2.5 Summary of the Analysis and Next Steps 3 Views on Set-Theoretic Semantics of Classical Predicate Logics 3.1 Tarskian Model Theory and Set-Theoretic Superstructure 3.2 Formal Semantics and Choices for Entity Postulation 3.3 Theory View of Semantics 3.4 Aims for an Ontologically Neutral Semantic Account 4 Ontological Semantics 4.1 Definition of Ontological Structures by Analogy to the Set-Theoretic Approach 4.2 Properties and Further Background for Ontological Structures in General 4.3 Ontological Models & Signature Aspects 4.4 Semantics of Predication 4.5 Semantics of Connectives and Quantifiers & Semantic Notions 4.6 Relations between Ontological and Set-Theoretic Semantics 4.7 Ontological Neutrality 5 Ontological Engineering and Applications 5.1 Formalization Method for Ontology Representation in FOL 5.2 Ontological Usage Schemes 5.3 Glimpse on Characterizing Modular Representation 5.4 Applications in the Biomedical Domain 6 Contributions to Ontologies 6.1 Formalizations of Categories and Relations - CR 6.2 Remarks on Further Contributions 6.3 Ontologies of Time 7 Conclusion and Continuation 7.1 Resume 7.2 Related Work 7.3 Conclusions 7.4 Beginnings of Future Work Appendix A Additional Preliminaries A.1 Logical Notions A.2 Axiomatic Systems of Set and Number Theory B Axioms of the CR Taxonomy in OWL B.1 Asserted OWL Class Axioms B.2 Asserted OWL Object Property Axioms C Lists of Figures and Tables C.1 List of Figures C.2 List of Tables D Abbreviations, Acronyms and Names D.1 Abbreviations D.2 Acronyms and Names E References E.1 Literature References E.2 Web References/List of URLs F Work and Author Information ** Selbständigkeitserklärung (Declaration of Authorship) ** Bibliographic Data ** Scientific Recor