254 research outputs found

    Cross-Product Extensions of the Gene Ontology

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    The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries

    Novel Algorithms for Cross-Ontology Multi-Level Data Mining

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    The wide spread use of ontologies in many scientific areas creates a wealth of ontologyannotated data and necessitates the development of ontology-based data mining algorithms. We have developed generalization and mining algorithms for discovering cross-ontology relationships via ontology-based data mining. We present new interestingness measures to evaluate the discovered cross-ontology relationships. The methods presented in this dissertation employ generalization as an ontology traversal technique for the discovery of interesting and informative relationships at multiple levels of abstraction between concepts from different ontologies. The generalization algorithms combine ontological annotations with the structure and semantics of the ontologies themselves to discover interesting crossontology relationships. The first algorithm uses the depth of ontological concepts as a guide for generalization. The ontology annotations are translated to higher levels of abstraction one level at a time accompanied by incremental association rule mining. The second algorithm conducts a generalization of ontology terms to all their ancestors via transitive ontology relations and then mines cross-ontology multi-level association rules from the generalized transactions. Our interestingness measures use implicit knowledge conveyed by the relation semantics of the ontologies to capture the usefulness of cross-ontology relationships. We describe the use of information theoretic metrics to capture the interestingness of cross-ontology relationships and the specificity of ontology terms with respect to an annotation dataset. Our generalization and data mining agorithms are applied to the Gene Ontology and the postnatal Mouse Anatomy Ontology. The results presented in this work demonstrate that our generalization algorithms and interestingness measures discover more interesting and better quality relationships than approaches that do not use generalization. Our algorithms can be used by researchers and ontology developers to discover inter-ontology connections. Additionally, the cross-ontology relationships discovered using our algorithms can be used by researchers to understand different aspects of entities that interest them

    An Algorithmic Approach to Inferring Cross-Ontology Links while Mapping Anatomical Ontologies

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    ACM Computing Classification System (1998): J.3.Automated and semi-automated mapping and the subsequently merging of two (or more) anatomical ontologies can be achieved by (at least) two direct procedures. The first concerns syntactic matching between the terms of the two ontologies; in this paper, we call this direct matching (DM). It relies on identities between the terms of the two input ontologies in order to establish cross-ontology links between them. The second involves consulting one or more external knowledge sources and utilizing the information available in them, thus providing additional information as to how terms (concepts) from the two input ontologies are related/linked to each other. Each of the two ontologies is aligned to an external knowledge source and links representing synonymy, is-a parent-child, and part-of parent-child relations, are drawn between the ontology and the knowledge source. These links are then run through a set of simple logical rules in order to come up with cross-ontology links between the two input ontologies. This method is known as semantic matching. It proves usefu

    Bridging the gap between folksonomies and the semantic web: an experience report

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    Abstract. While folksonomies allow tagging of similar resources with a variety of tags, their content retrieval mechanisms are severely hampered by being agnostic to the relations that exist between these tags. To overcome this limitation, several methods have been proposed to find groups of implicitly inter-related tags. We believe that content retrieval can be further improved by making the relations between tags explicit. In this paper we propose the semantic enrichment of folksonomy tags with explicit relations by harvesting the Semantic Web, i.e., dynamically selecting and combining relevant bits of knowledge from online ontologies. Our experimental results show that, while semantic enrichment needs to be aware of the particular characteristics of folksonomies and the Semantic Web, it is beneficial for both.

    Using concept similarity in cross ontology for adaptive e-Learning systems

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    Abstracte-Learning is one of the most preferred media of learning by the learners. The learners search the web to gather knowledge about a particular topic from the information in the repositories. Retrieval of relevant materials from a domain can be easily implemented if the information is organized and related in some way. Ontologies are a key concept that helps us to relate information for providing the more relevant lessons to the learner. This paper proposes an adaptive e-Learning system, which generates a user specific e-Learning content by comparing the concepts with more than one system using similarity measures. A cross ontology measure is defined, which consists of fuzzy domain ontology as the primary ontology and the domain expert’s ontology as the secondary ontology, for the comparison process. A personalized document is provided to the user with a user profile, which includes the data obtained from the processing of the proposed method under a User score, which is obtained through the user evaluation. The results of the proposed e-Learning system under the designed cross ontology similarity measure show a significant increase in performance and accuracy under different conditions. The assessment of the comparative analysis, showed the difference in performance of our proposed method over other methods. Based on the assessment results it is proved that the proposed approach is effective over other methods

    Ontology (Science)

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    Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type – the Gene Ontology (GO) being the most conspicuous example – are a _part of science_. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology develop¬ment work being undertaken in support of scientific research. Ontologies created by scientists must, of course, be associated with implementations satisfying the requirements of software engineering. But the ontologies are not themselves engineering artifacts, and to conceive them as such brings grievous consequences. Rather, ontologies such as the GO are in different respects comparable to scientific theories, to scientific databases, and to scientific journal publications. Such a view implies a new conception of what is involved in the author¬ing, maintenance and application of ontologies in scientific contexts, and therewith also a new approach to the evaluation of ontologies and to the training of ontologists

    Automated Annotation-Based Bio-Ontology Alignment with Structural Validation

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    We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations, and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes implicated in lung disease against the Gene Ontology

    The Gene Ontology in 2010: extensions and refinements

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    The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use
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