The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform, and new ontologies being created, on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved in the future

Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology

<p>Abstract</p> <p>Background</p> <p>Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologies is a prior condition for diverse and efficient reasoning, and hence querying and hypothesis validation. Rigour allows a more consistent maintenance. Modelling such bio-ontologies is, however, a difficult task for bio-ontologists, because the necessary richness and rigour is difficult to achieve without extensive training.</p> <p>Results</p> <p>Analogous to design patterns in software engineering, Ontology Design Patterns are solutions to typical modelling problems that bio-ontologists can use when building bio-ontologies. They offer a means of creating rich and rigorous bio-ontologies with reduced effort. The concept of Ontology Design Patterns is described and documentation and application methodologies for Ontology Design Patterns are presented. Some real-world use cases of Ontology Design Patterns are provided and tested in the Cell Cycle Ontology. Ontology Design Patterns, including those tested in the Cell Cycle Ontology, can be explored in the Ontology Design Patterns public catalogue that has been created based on the documentation system presented (<url>http://odps.sourceforge.net/</url>).</p> <p>Conclusions</p> <p>Ontology Design Patterns provide a method for rich and rigorous modelling in bio-ontologies. They also offer advantages at different development levels (such as design, implementation and communication) enabling, if used, a more modular, well-founded and richer representation of the biological knowledge. This representation will produce a more efficient knowledge management in the long term.</p

Dwelling on ontology - semantic reasoning over topographic maps

The thesis builds upon the hypothesis that the spatial arrangement of topographic features, such as buildings, roads and other land cover parcels, indicates how land is used. The aim is to make this kind of high-level semantic information explicit within topographic data. There is an increasing need to share and use data for a wider range of purposes, and to make data more definitive, intelligent and accessible. Unfortunately, we still encounter a gap between low-level data representations and high-level concepts that typify human qualitative spatial reasoning. The thesis adopts an ontological approach to bridge this gap and to derive functional information by using standard reasoning mechanisms offered by logic-based knowledge representation formalisms. It formulates a framework for the processes involved in interpreting land use information from topographic maps. Land use is a high-level abstract concept, but it is also an observable fact intimately tied to geography. By decomposing this relationship, the thesis correlates a one-to-one mapping between high-level conceptualisations established from human knowledge and real world entities represented in the data. Based on a middle-out approach, it develops a conceptual model that incrementally links different levels of detail, and thereby derives coarser, more meaningful descriptions from more detailed ones. The thesis verifies its proposed ideas by implementing an ontology describing the land use ‘residential area’ in the ontology editor Protégé. By asserting knowledge about high-level concepts such as types of dwellings, urban blocks and residential districts as well as individuals that link directly to topographic features stored in the database, the reasoner successfully infers instances of the defined classes. Despite current technological limitations, ontologies are a promising way forward in the manner we handle and integrate geographic data, especially with respect to how humans conceptualise geographic space

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

An ontological approach to the study of European popular culture

Like any other field of contemporary scholarly research, the Humanities in general, and Cultural Studies in particular are today confronted with the challenges of complexity at an unprecedented scale. What has been described as the \u201castonishing growth\u201d of academic publications worldwide is paralleled by a similar proliferation of browsable online databases, like digital archives, collections and catalogues, which offer access to an immense and continuously increasing volume of virtually interesting research material, stored in the form of information bytes. As we discussed in Deliverable 2.1, \u201cSorting out the archive for the study of European popular culture\u201d, the problem of how to cope with such an unseizable of virtually relevant sources of evidence is all the more sensible in the case of a project like DETECt, which deals with one of the most prolific narrative genres of contemporary media production, that is, the European crime narrative genre. Not only an exhaustive catalogue of this production could easily count\u2014especially when considered in all of its transnational scope\u2014in thousands of thousands, and even\u2014in historical perspective\u2014millions of items, but the transdisciplinary scope of the studies it has inspired has produced a wealth of research in many domains of knowledge. These difficult challenges make DETECt an ideal laboratory for experimenting new methods to manage complexity in a transnational/transcultural research environment. This methodological experimentation aims to respond to the problem of how to generate effective syntheses of portions and/or aspects of a given knowledge domain in a context of information overload. To this purpose, the ontological approach chosen by DETECt focuses on the application of knowledge mapping techniques to encourage the formulation of partial knowledge syntheses within a \u201crealist\u201d, and even \u201cpragmatic\u201d theoretical framework

Metaphor, Imagery, and Culture. Spatialized Ontologies, Mental Tools, and Multimedia in the Making.

The thesis deals with metaphor and imagery in cultural thought-models, the aim being an integrative framework for a rapprochement between cognitive science, cultural anthropology , and linguistics. The work couches previous ethnographic data in the theoretical apparatus of cognitive linguistics (as pioneered by G. Lakoff and R. Langacker), which is horizontally extended to include non-linguistic phenomena and vertically extended to include high-level mental tools. As groundwork for understanding cultural cognition in Part One I undertake a reappraisal of the theory of conceptual metaphor from a genuinely anthropological perspective: I elaborate (1) the multiplicity of metaphor's socio-cognitive functions, its embedding in complex 'polytropes', and its interplay with higher-level cultural schemas; (2)I propose a balanced view between universality and cultural variation in metaphor; and (3) I advocate an intensified focus on cultural body knowledge as the basis of metaphor. Part Two sets as its goal to contour the scope of cultural imagery by extending the theory of dynamic image schemas, as laid out by Langacker, beyond language itself: (4) I analyze essentialist and processual ontologies as being defined through basic imagery types and dynamic switches between ontologies through image schema transformations. (5) Next, I argue for the necessity of cognitive multimedia analysis and offer a model based on the presupposition that various aspects of language, non-linguistic symbolism, action schemas, and body feelings operate in a continuous mental substrate, namely image schemas. (6) Finally, taking the lead from Lakoff's 'spatialization of form' hypothesis, I challenge the broader cognitive sciences with a multi-level theory of spatialized ('geometric') imagery that spans from semantics to general-purpose mental 'tools'. Its upshot is a relativization of symbolic or propositional approaches to thought as well as faculty psychology