Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

A Heuristic Ontological Model of Protein Complexes A Case Study Based on the E3 Ubiquitin Ligase Protein Complexes of Arabidopsis thaliana

Ontology (with a capital O) is the philosophical study of the nature of existence that was derived to define the relationships of entities that can be said to exist in nature. The concept of an ontology was later adopted by the biological sciences to formally represent knowledge within a biological domain in order to standardize the annotation of biological data, and further, enable more efficient and easier data collection, sharing, and reuse across biological and model organism databases. The Protein Ontology (PRO) is a specific biological ontology developed to represent the relationships between proteins and protein complexes. This thesis presents a revised PRO framework, modelled around Arabidopsis thaliana and associated SCF ubiquitin ligase complexes, with the aim to more adequately represent what is known about the process and dynamics of protein complex formation in order to better serve the broader scientific community

Enriching the Functionally Graded Materials (FGM) Ontology for digital manufacturing

Functionally graded materials (FGMs) have been used in many different kinds of applications in recent years and have attracted significant research attention. However, we do not yet have a commonly accepted way of representing the various aspects of FGMs. Lack of standardised vocabulary creates obstacles to the extraction of useful information relating to pertinent aspects of different applications. A standard resource is needed for describing various elements of FGMs, including existing applications, manufacturing techniques, and material characteristics. This motivated the creation of the FGM Ontology (FGMO) in 2016. Here, we present a revised and expanded version of the FGM Ontology, which includes enrichments along four dimensions: (1) documenting recent FGMs applications; (2) reorganising the framework to incorporate an updated representation of types of manufacturing processes; (3) enriching the axioms of the ontology; and (4) importing mid-level ontologies from the Common Core Ontologies (CCO) and Product Life Cycle (PLC) Ontologies. The work is being carried out within the framework of the Industry Ontology Foundry (IOF), and the ontology is conformant to Basic Formal Ontology (BFO)

Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

The Gene Ontology Handbook

bioinformatics; biotechnolog

Abstract Representation of Music: A Type-Based Knowledge Representation Framework

The wholesale efficacy of computer-based music research is contingent on the sharing and reuse of information and analysis methods amongst researchers across the constituent disciplines. However, computer systems for the analysis and manipulation of musical data are generally not interoperable. Knowledge representation has been extensively used in the domain of music to harness the benefits of formal conceptual modelling combined with logic based automated inference. However, the available knowledge representation languages lack sufficient logical expressivity to support sophisticated musicological concepts. In this thesis we present a type-based framework for abstract representation of musical knowledge. The core of the framework is a multiple-hierarchical information model called a constituent structure, which accommodates diverse kinds of musical information. The framework includes a specification logic for expressing formal descriptions of the components of the representation. We give a formal specification for the framework in the Calculus of Inductive Constructions, an expressive logical language which lends itself to the abstract specification of data types and information structures. We give an implementation of our framework using Semantic Web ontologies and JavaScript. The ontologies capture the core structural aspects of the representation, while the JavaScript tools implement the functionality of the abstract specification. We describe how our framework supports three music analysis tasks: pattern search and discovery, paradigmatic analysis and hierarchical set-class analysis, detailing how constituent structures are used to represent both the input and output of these analyses including sophisticated structural annotations. We present a simple demonstrator application, built with the JavaScript tools, which performs simple analysis and visualisation of linked data documents structured by the ontologies. We conclude with a summary of the contributions of the thesis and a discussion of the type-based approach to knowledge representation, as well as a number of avenues for future work in this area

Mesures sémantiques à base de connaissance : de la théorie aux applicatifs

The notions of semantic proximity, distance, and similarity have long been considered essential for the elaboration of numerous cognitive processes, and are therefore of major importance for the communities involved in the development of artificial intelligence. This thesis studies the diversity of semantic measures which can be used to compare lexical entities, concepts and instances by analysing corpora of texts and ontologies. Strengthened by the development of Knowledge Representation and Semantic Web technologies, these measures are arousing increasing interest in both academic and industrial fields.This manuscript begins with an extensive state-of-the-art which presents numerous contributions proposed by several communities, and underlines the diversity and interdisciplinary nature of this domain. Thanks to this work, despite the apparent heterogeneity of semantic measures, we were able to distinguish common properties and therefore propose a general classification of existing approaches. Our work goes on to look more specifically at measures which take advantage of ontologies expressed by means of semantic graphs, e.g. RDF(S) graphs. We show that these measures rely on a reduced set of abstract primitives and that, even if they have generally been defined independently in the literature, most of them are only specific expressions of generic parametrised measures. This result leads us to the definition of a unifying theoretical framework for semantic measures, which can be used to: (i) design new measures, (ii) study theoretical properties of measures, (iii) guide end-users in the selection of measures adapted to their usage context. The relevance of this framework is demonstrated in its first practical applications which show, for instance, how it can be used to perform theoretical and empirical analyses of measures with a previously unattained level of detail. Interestingly, this framework provides a new insight into semantic measures and opens interesting perspectives for their analysis.Having uncovered a flagrant lack of generic and efficient software solutions dedicated to (knowledge-based) semantic measures, a lack which clearly hampers both the use and analysis of semantic measures, we consequently developed the Semantic Measures Library (SML): a generic software library dedicated to the computation and analysis of semantic measures. The SML can be used to take advantage of hundreds of measures defined in the literature or those derived from the parametrised functions introduced by the proposed unifying framework. These measures can be analysed and compared using the functionalities provided by the library. The SML is accompanied by extensive documentation, community support and software solutions which enable non-developers to take full advantage of the library. In broader terms, this project proposes to federate the several communities involved in this domain in order to create an interdisciplinary synergy around the notion of semantic measures: http://www.semantic-measures-library.org This thesis also presents several algorithmic and theoretical contributions related to semantic measures: (i) an innovative method for the comparison of instances defined in a semantic graph - we underline in particular its benefits in the definition of content-based recommendation systems, (ii) a new approach to compare concepts defined in overlapping taxonomies, (iii) algorithmic optimisation for the computation of a specific type of semantic measure, and (iv) a semi-supervised learning-technique which can be used to identify semantic measures adapted to a specific usage context, while simultaneously taking into account the uncertainty associated to the benchmark in use. These contributions have been validated by several international and national publications.Les notions de proximité, de distance et de similarité sémantiques sont depuis longtemps jugées essentielles dans l’élaboration de nombreux processus cognitifs et revêtent donc un intérêt majeur pour les communautés intéressées au développement d'intelligences artificielles. Cette thèse s'intéresse aux différentes mesures sémantiques permettant de comparer des unités lexicales, des concepts ou des instances par l'analyse de corpus de textes ou de représentations de connaissance (i.e. ontologies). Encouragées par l'essor des technologies liées à l'Ingénierie des Connaissances et au Web sémantique, ces mesures suscitent de plus en plus d'intérêt à la fois dans le monde académique et industriel.Ce manuscrit débute par un vaste état de l'art qui met en regard des travaux publiés dans différentes communautés et souligne l'aspect interdisciplinaire et la diversité des recherches actuelles dans ce domaine. Cela nous a permis, sous l'apparente hétérogénéité des mesures existantes, de distinguer certaines propriétés communes et de présenter une classification générale des approches proposées. Par la suite, ces travaux se concentrent sur les mesures qui s'appuient sur une structuration de la connaissance sous forme de graphes sémantiques, e.g. graphes RDF(S). Nous montrons que ces mesures reposent sur un ensemble réduit de primitives abstraites, et que la plupart d'entre elles, bien que définies indépendamment dans la littérature, ne sont que des expressions particulières de mesures paramétriques génériques. Ce résultat nous a conduits à définir un cadre théorique unificateur pour les mesures sémantiques. Il permet notamment : (i) d'exprimer de nouvelles mesures, (ii) d'étudier les propriétés théoriques des mesures et (iii) d'orienter l'utilisateur dans le choix d'une mesure adaptée à sa problématique. Les premiers cas concrets d'utilisation de ce cadre démontrent son intérêt en soulignant notamment qu'il permet l'analyse théorique et empirique des mesures avec un degré de détail particulièrement fin, jamais atteint jusque-là. Plus généralement, ce cadre théorique permet de poser un regard neuf sur ce domaine et ouvre de nombreuses perspectives prometteuses pour l'analyse des mesures sémantiques.Le domaine des mesures sémantiques souffre d'un réel manque d'outils logiciels génériques et performants ce qui complique à la fois l'étude et l'utilisation de ces mesures. En réponse à ce manque, nous avons développé la Semantic Measures Library (SML), une librairie logicielle dédiée au calcul et à l'analyse des mesures sémantiques. Elle permet d'utiliser des centaines de mesures issues à la fois de la littérature et des fonctions paramétriques étudiées dans le cadre unificateur introduit. Celles-ci peuvent être analysées et comparées à l'aide des différentes fonctionnalités proposées par la librairie. La SML s'accompagne d'une large documentation, d'outils logiciels permettant son utilisation par des non informaticiens, d'une liste de diffusion, et de façon plus large, se propose de fédérer les différentes communautés du domaine afin de créer une synergie interdisciplinaire autour la notion de mesures sémantiques : http://www.semantic-measures-library.orgCette étude a également conduit à différentes contributions algorithmiques et théoriques, dont (i) la définition d'une méthode innovante pour la comparaison d'instances définies dans un graphe sémantique - nous montrons son intérêt pour la mise en place de système de recommandation à base de contenu, (ii) une nouvelle approche pour comparer des concepts représentés dans des taxonomies chevauchantes, (iii) des optimisations algorithmiques pour le calcul de certaines mesures sémantiques, et (iv) une technique d'apprentissage semi-supervisée permettant de cibler les mesures sémantiques adaptées à un contexte applicatif particulier en prenant en compte l'incertitude associée au jeu de test utilisé. Ces travaux ont été validés par plusieurs publications et communications nationales et internationales

A semantic framework for ontology usage analysis

The Semantic Web envisions a Web where information is accessible and processable by computers as well as humans. Ontologies are the cornerstones for realizing this vision of the Semantic Web by capturing domain knowledge by defining the terms and the relationship between these terms to provide a formal representation of the domain with machine-understandable semantics. Ontologies are used for semantic annotation, data interoperability and knowledge assimilation and dissemination.In the literature, different approaches have been proposed to build and evolve ontologies, but in addition to these, one more important concept needs to be considered in the ontology lifecycle, that is, its usage. Measuring the “usage” of ontologies will help us to effectively and efficiently make use of semantically annotated structured data published on the Web (formalized knowledge published on the Web), improve the state of ontology adoption and reusability, provide a usage-based feedback loop to the ontology maintenance process for a pragmatic conceptual model update, and source information accurately and automatically which can then be utilized in the other different areas of the ontology lifecycle. Ontology Usage Analysis is the area which evaluates, measures and analyses the use of ontologies on the Web. However, in spite of its importance, no formal approach is present in the literature which focuses on measuring the use of ontologies on the Web. This is in contrast to the approaches proposed in the literature on the other concepts of the ontology lifecycle, such as ontology development, ontology evaluation and ontology evolution. So, to address this gap, this thesis is an effort in such a direction to assess, analyse and represent the use of ontologies on the Web.In order to address the problem and realize the abovementioned benefits, an Ontology Usage Analysis Framework (OUSAF) is presented. The OUSAF Framework implements a methodological approach which is comprised of identification, investigation, representation and utilization phases. These phases provide a complete solution for usage analysis by allowing users to identify the key ontologies, and investigate, represent and utilize usage analysis results. Various computation components with several methods, techniques, and metrics for each phase are presented and evaluated using the Semantic Web data crawled from the Web. For the dissemination of ontology-usage-related information accessible to machines and humans, The U Ontology is presented to formalize the conceptual model of the ontology usage domain. The evaluation of the framework, solution components, methods, and a formalized conceptual model is presented, indicating the usefulness of the overall proposed solution