Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

A Model-Driven Approach for the Design, Implementation, and Execution of Software Development Methods

[EN] Software development projects are diverse in nature. For this reason, software companies are often forced to define their methods in-house. In order to define methods efficiently and effectively, software companies require systematic solutions that are built upon sound methodical foundations. Providing these solutions is the main goal of the Method Engineering discipline. Method Engineering is the discipline to design, construct, and adapt methods, techniques, and tools for the development of information systems. Over the last two decades, a lot of research work has been performed in this area. However, despite its potential benefits, Method Engineering is not widely used in industrial settings. Some of the causes of this reality are the high theoretical complexity of Method Engineering and the lack of adequate software support. In this thesis, we aim to mitigate some of the problems that affect Method Engineering by providing a novel methodological approach that is built upon Model-Driven Engineering (MDE) foundations. The use of MDE enables a rise in abstraction, automation, and reuse that allows us to alleviate the complexity of our Method Engineering approach. Furthermore, by leveraging MDE techniques (such as metamodeling, model transformations, and models at runtime), our approach supports three phases of the Method Engineering lifecycle: design, implementation, and execution. This is unlike traditional Method Engineering approaches, which, in general, only support one of these phases. In order to provide software support for our proposal, we developed a Computer-Aided Method Engineering (CAME) environment that is called MOSKitt4ME. To ensure that MOSKitt4ME offered the necessary functionality, we identified a set of functional requirements prior to developing the tool. Then, after these requirements were identified, we defined the architecture of our CAME environment, and, finally, we implemented the architecture in the context of Eclipse. The thesis work was evaluated by means of a study that involved the participation of end users. In this study, MOSKitt4ME was assessed by means of the Technology Acceptance Model (TAM) and the Think Aloud method. While the TAM allowed us to measure usefulness and ease of use in a subjective manner, the Think Aloud method allowed us to analyze these measures objectively. Overall, the results were favorable. MOSKitt4ME was highly rated in perceived usefulness and ease of use; we also obtained positive results with respect to the users' actual performance and the difficulty experienced.[ES] Los proyectos de desarrollo de software son diversos por naturaleza. Por este motivo, las compañías de software se ven forzadas frecuentemente a definir sus métodos de manera interna. Para poder definir métodos de forma efectiva y eficiente, las compañías necesitan soluciones sistemáticas que estén definidas sobre unos fundamentos metodológicos sólidos. Proporcionar estas soluciones es el principal objetivo de la Ingeniería de Métodos. La Ingeniería de Métodos es la disciplina que aborda el diseño, la construcción y la adaptación de métodos, técnicas y herramientas para el desarrollo de sistemas de información. Durante las dos últimas décadas, se ha llevado a cabo mucho trabajo de investigación en esta área. Sin embargo, pese a sus potenciales beneficios, la Ingeniería de Métodos no se aplica ampliamente en contextos industriales. Algunas de las principales causas de esta situación son la alta complejidad teórica de la Ingeniería de Métodos y la falta de un apropiado soporte software. En esta tesis, pretendemos mitigar algunos de los problemas que afectan a la Ingeniería de Métodos proporcionando una propuesta metodológica innovadora que está basada en la Ingeniería Dirigida por Modelos (MDE). El uso de MDE permite elevar el nivel de abstracción, automatización y reuso, lo que posibilita una reducción de la complejidad de nuestra propuesta. Además, aprovechando técnicas de MDE (como por ejemplo el metamodelado, las transformaciones de modelos y los modelos en tiempo de ejecución), nuestra aproximación da soporte a tres fases del ciclo de vida de la Ingeniería de Métodos: diseño, implementación y ejecución. Esto es a diferencia de las propuestas existentes, las cuales, por lo general, sólo dan soporte a una de estas fases. Con el objetivo de proporcionar soporte software para nuestra propuesta, implementamos una herramienta CAME (Computer-Aided Method Engineering) llamada MOSKitt4ME. Para garantizar que MOSKitt4ME proporcionaba la funcionalidad necesaria, definimos un conjunto de requisitos funcionales como paso previo al desarrollo de la herramienta. Tras la definción de estos requisitos, definimos la arquitectura de la herramienta CAME y, finalmente, implementamos la arquitectura en el contexto de Eclipse. El trabajo desarrollado en esta tesis se evaluó por medio de un estudio donde participaron usuarios finales. En este estudio, MOSKitt4ME se evaluó por medio del Technology Acceptance Model (TAM) y del método Think Aloud. Mientras que el TAM permitió medir utilidad y facilidad de uso de forma subjetiva, el método Think Aloud permitió analizar estas medidas objetivamente. En general, los resultados obtenidos fueron favorables. MOSKitt4ME fue valorado de forma positiva en cuanto a utilidad y facilidad de uso percibida; además, obtuvimos resultados positivos en cuanto al rendimiento objetivo de los usuarios y la dificultad experimentada.[CA] Els projectes de desenvolupament de programari són diversos per naturalesa. Per aquest motiu, les companyies es veuen forçades freqüenment a definir els seus mètodes de manera interna. Per poder definir mètodes de forma efectiva i eficient, les companyies necessiten solucions sistemàtiques que estiguin definides sobre uns fundaments metodològics sòlids. Proporcionar aquestes solucions és el principal objectiu de l'Enginyeria de Mètodes. L'Enginyeria de Mètodes és la disciplina que aborda el diseny, la construcció i l'adaptació de mètodes, tècniques i eines per al desenvolupament de sistemes d'informació. Durant les dues últimes dècades, s'ha dut a terme molt de treball de recerca en aquesta àrea. No obstant, malgrat els seus potencials beneficis, l'Enginyeria de Mètodes no s'aplica àmpliament en contextes industrials. Algunes de les principals causes d'aquesta situació són l'alta complexitat teòrica de l'Enginyeria de Mètodes i la falta d'un apropiat suport de programari. En aquesta tesi, pretenem mitigar alguns dels problemes que afecten a l'Enginyeria de Mètodes proporcionant una proposta metodològica innovadora que està basada en l'Enginyeria Dirigida per Models (MDE). L'ús de MDE ens permet elevar el nivell d'abstracció, automatització i reutilització, possibilitant una reducció de la complexitat de la nostra proposta. A més a més, aprofitant tècniques de MDE (com per exemple el metamodelat, les transformacions de models i els models en temps d'execució), la nostra aproximació suporta tres fases del cicle de vida de l'Enginyeria de Mètodes: diseny, implementació i execució. Açò és a diferència de les propostes existents, les quals, en general, només suporten una d'aquestes fases. Amb l'objectiu de proporcionar suport de programari per a la nostra proposta, implementàrem una eina CAME (Computer-Aided Method Engineering) anomenada MOSKitt4ME. Per garantir que MOSKitt4ME oferia la funcionalitat necessària, definírem un conjunt de requisits funcionals com a pas previ al desenvolupament de l'eina. Després de la definició d'aquests requisits, definírem la arquitectura de l'eina CAME i, finalment, implementàrem l'arquitectura en el contexte d'Eclipse. El treball desenvolupat en aquesta tesi es va avaluar per mitjà d'un estudi on van participar usuaris finals. En aquest estudi, MOSKitt4ME es va avaluar per mitjà del Technology Acceptance Model (TAM) i el mètode Think Aloud. Mentre que el TAM va permetre mesurar utilitat i facilitat d'ús de manera subjectiva, el mètode Think Aloud va permetre analitzar aquestes mesures objectivament. En general, els resultats obtinguts van ser favorables. MOSKitt4ME va ser valorat de forma positiva pel que fa a utilitat i facilitat d'ús percebuda; a més a més, vam obtenir resultats positius pel que fa al rendiment objectiu dels usuaris i a la dificultat experimentada.Cervera Úbeda, M. (2015). A Model-Driven Approach for the Design, Implementation, and Execution of Software Development Methods [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/53931TESI

Providing end-user facilities to simplify ontology-driven web application authoring

This is the author’s version of a work that was accepted for publication in Interacting with Computers. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Interacting with Computers, Interacting with Computers 17, 4 (2007) DOI: 10.1016/j.intcom.2007.01.006Generally speaking, emerging web-based technologies are mostly intended for professional developers. They pay poor attention to users who have no programming abilities but need to customize software applications. At some point, such needs force end-users to act as designers in various aspects of software authoring and development. Every day, more new computing-related professionals attempt to create and modify existing applications in order to customize web-based artifacts that will help them carry out their daily tasks. In general they are domain experts rather than skilled software designers, and new authoring mechanisms are needed in order that they can accomplish their tasks properly. The work we present is an effort to supply end-users with easy mechanisms for authoring web-based applications. To complement this effort, we present a user study showing that it is possible to carry out a trade-off between expressiveness and ease of use in order to provide end-users with authoring facilities.The work reported in this paper is being partially supported by the Spanish Ministry of Science and Technology (MCyT), projects TIN2005-06885 and TSI2005-08225-C07-06

Method and System for Identification of Metabolites Using Mass Spectra

A method and system is provided for mass spectrometry for identification of a specific elemental formula for an unknown compound which includes but is not limited to a metabolite. The method includes calculating a natural abundance probability (NAP) of a given isotopologue for isotopes of non-labelling elements of an unknown compound. Molecular fragments for a subset of isotopes identified using the NAP are created and sorted into a requisite cache data structure to be subsequently searched. Peaks from raw spectrum data from mass spectrometry for an unknown compound. Sample-specific peaks of the unknown com- pound from various spectral artifacts in ultra-high resolution Fourier transform mass spectra are separated. A set of possible isotope-resolved molecular formula (IMF) are created by iteratively searching the molecular fragment caches and combining with additional isotopes and then statistically filtering the results based on NAP and mass-to-charge (m/2) matching probabilities. An unknown compound is identified and its corresponding elemental molecular formula (EMF) from statistically-significant caches of isotopologues with compatible IMFs

Emergent Rhythmic Structures as Cultural Phenomena Driven by Social Pressure in a Society of Artificial Agents

This thesis studies rhythm from an evolutionary computation perspective. Rhythm is the most fundamental dimension of music and can be used as a ground to describe the evolution of music. More specifically, the main goal of the thesis is to investigate how complex rhythmic structures evolve, subject to the cultural transmission between individuals in a society. The study is developed by means of computer modelling and simulations informed by evolutionary computation and artificial life (A-Life). In this process, self-organisation plays a fundamental role. The evolutionary process is steered by the evaluation of rhythmic complexity and by the exposure to rhythmic material. In this thesis, composers and musicologists will find the description of a system named A-Rhythm, which explores the emerged behaviours in a community of artificial autonomous agents that interact in a virtual environment. The interaction between the agents takes the form of imitation games. A set of necessary criteria was established for the construction of a compositional system in which cultural transmission is observed. These criteria allowed the comparison with related work in the field of evolutionary computation and music. In the development of the system, rhythmic representation is discussed. The proposed representation enabled the development of complexity and similarity based measures, and the recombination of rhythms in a creative manner. A-Rhythm produced results in the form of simulation data which were evaluated in terms of the coherence of repertoires of the agents. The data shows how rhythmic sequences are changed and sustained in the population, displaying synchronic and diachronic diversity. Finally, this tool was used as a generative mechanism for composition and several examples are presented.Leverhulme Trus