Internet based molecular collaborative and publishing tools

The scientific electronic publishing model has hitherto been an Internet based delivery of electronic articles that are essentially replicas of their paper counterparts. They contain little in the way of added semantics that may better expose the science, assist the peer review process and facilitate follow on collaborations, even though the enabling technologies have been around for some time and are mature. This thesis will examine the evolution of chemical electronic publishing over the past 15 years. It will illustrate, which the help of two frameworks, how publishers should be exploiting technologies to improve the semantics of chemical journal articles, namely their value added features and relationships with other chemical resources on the Web. The first framework is an early exemplar of structured and scalable electronic publishing where a Web content management system and a molecular database are integrated. It employs a test bed of articles from several RSC journals and supporting molecular coordinate and connectivity information. The value of converting 3D molecular expressions in chemical file formats, such as the MOL file, into more generic 3D graphics formats, such as Web3D, is assessed. This exemplar highlights the use of metadata management for bidirectional hyperlink maintenance in electronic publishing. The second framework repurposes this metadata management concept into a Semantic Web application called SemanticEye. SemanticEye demonstrates how relationships between chemical electronic articles and other chemical resources are established. It adapts the successful semantic model used for digital music metadata management by popular applications such as iTunes. Globally unique identifiers enable relationships to be established between articles and other resources on the Web and SemanticEye implements two: the Document Object Identifier (DOI) for articles and the IUPAC International Chemical Identifier (InChI) for molecules. SemanticEye’s potential as a framework for seeding collaborations between researchers, who have hitherto never met, is explored using FOAF, the friend-of-a-friend Semantic Web standard for social networks

DRIVER Technology Watch Report

This report is part of the Discovery Workpackage (WP4) and is the third report out of four deliverables. The objective of this report is to give an overview of the latest technical developments in the world of digital repositories, digital libraries and beyond, in order to serve as theoretical and practical input for the technical DRIVER developments, especially those focused on enhanced publications. This report consists of two main parts, one part focuses on interoperability standards for enhanced publications, the other part consists of three subchapters, which give a landscape picture of current and surfacing technologies and communities crucial to DRIVER. These three subchapters contain the GRID, CRIS and LTP communities and technologies. Every chapter contains a theoretical explanation, followed by case studies and the outcomes and opportunities for DRIVER in this field

HealthCyberMap: Mapping the Health Cyberspace Using Hypermedia GIS and Clinical Codes

HealthCyberMap () is a Semantic Web service for healthcare professionals and librarians, patients and the public m general that aims at mappmg parts of medical/ health information resources in cyberspace in novel ways to improve their retrieval and navigation. The Semantic Web ( and ) aims to be the next-generation World Wide Web by giving machine-readable semantics and context to the currently presentation-based Web pages. HealthCyberMap features an unconventional use of GIS (Geographic Information Systems) to map conceptual spaces occupied by collections of medical/ health information resources. Besides mapping the semantic and non-geographical aspects of these resources using suitable spatial metaphors, HealthCyberMap also collects and maps the geographical provenance of these resources. Some of HealthCyberMap Web interfaces are visual (maps for browsing resources by clinical/ health topic, by provenance and by type), while others are textual (multilingual interfaces for browsing resources by language, and a directory of topical resource categories, besides HealthCyberMap Semantic Subject Search Engine that goes beyond conventional free-text and keyword-based search engines, and supports synonyms, disease variants, subtypes, as well as some semantic relationships between terms). HealthCyberMap adopts a clinical metadata framework built upon a clinical coding scheme (vocabulary or ontology—ICD-9-CM* clinical classification in the current pilot service). Clinical coding schemes serve as a reliable common backbone for topical resource indexing, automated topical classification, topical visualisation and navigation of coded resource pools (using suitable metaphors), and enhanced information retrieval and linking. A resource metadata base based on Dublin Core metadata set with HealthCyberMap’s own extensions holds information about selected high-quality resources. HealthCyberMap then uses GIS spatialisation methods to generate interactive navigational cybermaps from the metadata base. These visual cybermaps are based on familiar metaphors for image-word association to give users a broad overview and understanding of what is available in this complex conceptual space of medical/ health Internet resources and help them navigate it more efficiently and effectively. HealthCyberMap cybermaps can be considered as semantically-spatialised, ontology-based browsing views of the underlying resource metadata base. Using a clinical coding scheme as a metric for spatialisation (“semantic distance”) is unique to HealthCyberMap and is very much suited for the semantic categorisation and navigation of medical/ health Internet information resources. HealthCyberMap also introduces a useful form of cyberspatial analysis for the detection of topical coverage gaps in its resource pool using choropleth (shaded) maps of human body systems. The project features a cost-effective method for serving Web hypermaps with dynamic metadata base drill-down functionality. It also demonstrates the feasibility of Electronic Patient Record to Online Information Services (like HealthCyberMap) Problem to Knowledge Linking using clinical codes as crisp problem-knowledge linkers or knowledge hooks. The Semantic Subject Search Engine queries the same HealthCyberMap resource metadata base. Explicit concepts in resource metadata map onto a brokering domain ontology (ICD-9-CM) allowing the search engine to infer implicit meanings (synonyms and semantic relationships) not directly mentioned in either the resource or its metadata. Similarly, user queries would map to the same ontology allowing the search engine to infer the implicit semantics of user queries and use them to optimise retrieval. A formative evaluation study of HealthCyberMap pilot service using an online user evaluation questionnaire, in addition to analysis of HealthCyberMap server transaction log, has been conducted during the period from 18 April 2002 to 1 June 2002 with very encouraging results. This two-method evaluation approach was guided by methodologies described in NIH Web Site Evaluation and Performance Measures Toolkit among other resources. Many exciting future possibilities have been also investigated by the author, including the further development of HealthCyberMap as a customisable, location-based medical/ health information service

Proceedings of the First International Workshop on Mashup Personal Learning Environments

Wild, F., Kalz, M., & Palmér, M. (Eds.) (2008). Proceedings of the First International Workshop on Mashup Personal Learning Environments (MUPPLE08). September, 17, 2008, Maastricht, The Netherlands: CEUR Workshop Proceedings, ISSN 1613-0073. Available at http://ceur-ws.org/Vol-388.The work on this publication has been sponsored by the TENCompetence Integrated Project (funded by the European Commission's 6th Framework Programme, priority IST/Technology Enhanced Learning. Contract 027087 [http://www.tencompetence.org]) and partly sponsored by the LTfLL project (funded by the European Commission's 7th Framework Programme, priority ISCT. Contract 212578 [http://www.ltfll-project.org

Semantic Federation of Musical and Music-Related Information for Establishing a Personal Music Knowledge Base

Music is perceived and described very subjectively by every individual. Nowadays, people often get lost in their steadily growing, multi-placed, digital music collection. Existing music player and management applications get in trouble when dealing with poor metadata that is predominant in personal music collections. There are several music information services available that assist users by providing tools for precisely organising their music collection, or for presenting them new insights into their own music library and listening habits. However, it is still not the case that music consumers can seamlessly interact with all these auxiliary services directly from the place where they access their music individually. To profit from the manifold music and music-related knowledge that is or can be available via various information services, this information has to be gathered up, semantically federated, and integrated into a uniform knowledge base that can personalised represent this data in an appropriate visualisation to the users. This personalised semantic aggregation of music metadata from several sources is the gist of this thesis. The outlined solution particularly concentrates on users’ needs regarding music collection management which can strongly alternate between single human beings. The author’s proposal, the personal music knowledge base (PMKB), consists of a client-server architecture with uniform communication endpoints and an ontological knowledge representation model format that is able to represent the versatile information of its use cases. The PMKB concept is appropriate to cover the complete information flow life cycle, including the processes of user account initialisation, information service choice, individual information extraction, and proactive update notification. The PMKB implementation makes use of SemanticWeb technologies. Particularly the knowledge representation part of the PMKB vision is explained in this work. Several new Semantic Web ontologies are defined or existing ones are massively modified to meet the requirements of a personalised semantic federation of music and music-related data for managing personal music collections. The outcome is, amongst others, • a new vocabulary for describing the play back domain, • another one for representing information service categorisations and quality ratings, and • one that unites the beneficial parts of the existing advanced user modelling ontologies. The introduced vocabularies can be perfectly utilised in conjunction with the existing Music Ontology framework. Some RDFizers that also make use of the outlined ontologies in their mapping definitions, illustrate the fitness in practise of these specifications. A social evaluation method is applied to carry out an examination dealing with the reutilisation, application and feedback of the vocabularies that are explained in this work. This analysis shows that it is a good practise to properly publish Semantic Web ontologies with the help of some Linked Data principles and further basic SEO techniques to easily reach the searching audience, to avoid duplicates of such KR specifications, and, last but not least, to directly establish a \"shared understanding\". Due to their project-independence, the proposed vocabularies can be deployed in every knowledge representation model that needs their knowledge representation capacities. This thesis added its value to make the vision of a personal music knowledge base come true.:1 Introduction and Background 11 1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 1.2 Personal Music Collection Use Cases . . . . . . . . . . . . . . . . . . . . . . . . . 14 1.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 2 Music Information Management 17 2.1 Knowledge Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 2.1.1 Knowledge Representation . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.1.1.1 Knowledge Representation Models . . . . . . . . . . . . . . . . . 18 2.1.1.2 Semantic Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . 18 2.1.1.3 Ontologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.1.1.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.1.2 Knowledge Management Systems . . . . . . . . . . . . . . . . . . . . . . . 19 2.1.2.1 Information Services . . . . . . . . . . . . . . . . . . . . . . . . . 19 2.1.2.2 Ontology-based Distributed Knowledge Management Systems . . 20 2.1.2.3 Knowledge Management System Design Guideline . . . . . . . . 21 2.1.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.2 Semantic Web Technologies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22 2.2.1 The Evolution of the World Wide Web . . . . . . . . . . . . . . . . . . . . . 22 Personal Music Knowledge Base Contents 2.2.1.1 The Hypertext Web . . . . . . . . . . . . . . . . . . . . . . . . . . 23 2.2.1.2 The Normative Principles of Web Architecture . . . . . . . . . . . 23 2.2.1.3 The Semantic Web . . . . . . . . . . . . . . . . . . . . . . . . . . 24 2.2.2 Common Semantic Web Knowledge Representation Languages . . . . . . 25 2.2.3 Resource Description Levels and their Relations . . . . . . . . . . . . . . . 26 2.2.4 Semantic Web Knowledge Representation Models . . . . . . . . . . . . . . 29 2.2.4.1 Construction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.2.4.2 Mapping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 2.2.4.3 Context Modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . 31 2.2.4.4 Storing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 2.2.4.5 Providing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 2.2.4.6 Consuming . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35 2.2.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 2.3 Music Content and Context Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 2.3.1 Categories of Musical Characteristics . . . . . . . . . . . . . . . . . . . . . 37 2.3.2 Music Metadata Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38 2.3.3 Music Metadata Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 2.3.3.1 Audio Signal Carrier Indexing Services . . . . . . . . . . . . . . . . 41 2.3.3.2 Music Recommendation and Discovery Services . . . . . . . . . . 42 2.3.3.3 Music Content and Context Analysis Services . . . . . . . . . . . 43 2.3.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 2.4 Personalisation and Environmental Context . . . . . . . . . . . . . . . . . . . . . . 44 2.4.1 User Modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44 2.4.2 Context Modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45 2.4.3 Stereotype Modelling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 2.5 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 3 The Personal Music Knowledge Base 48 3.1 Foundations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 3.1.1 Knowledge Representation . . . . . . . . . . . . . . . . . . . . . . . . . . . 48 3.1.2 Knowledge Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50 3.2 Architecture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 3.3 Workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 3.3.1 User Account Initialisation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 3.3.2 Individual Information Extraction . . . . . . . . . . . . . . . . . . . . . . . . 53 3.3.3 Information Service Choice . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 3.3.4 Proactive Update Notification . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.3.5 Information Exploration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55 3.3.6 Personal Associations and Context . . . . . . . . . . . . . . . . . . . . . . . 56 3.4 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56 4 A Personal Music Knowledge Base 57 4.1 Knowledge Representation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 4.1.1 The Info Service Ontology . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 4.1.2 The Play Back Ontology and related Ontologies . . . . . . . . . . . . . . . . 61 4.1.2.1 The Ordered List Ontology . . . . . . . . . . . . . . . . . . . . . . 61 4.1.2.2 The Counter Ontology . . . . . . . . . . . . . . . . . . . . . . . . . 62 4.1.2.3 The Association Ontology . . . . . . . . . . . . . . . . . . . . . . . 64 4.1.2.4 The Play Back Ontology . . . . . . . . . . . . . . . . . . . . . . . . 65 4.1.3 The Recommendation Ontology . . . . . . . . . . . . . . . . . . . . . . . . 69 4.1.4 The Cognitive Characteristics Ontology and related Vocabularies . . . . . . 72 4.1.4.1 The Weighting Ontology . . . . . . . . . . . . . . . . . . . . . . . 72 4.1.4.2 The Cognitive Characteristics Ontology . . . . . . . . . . . . . . . 73 4.1.4.3 The Property Reification Vocabulary . . . . . . . . . . . . . . . . . 78 4.1.5 The Media Types Taxonomy . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 4.1.6 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 4.2 Knowledge Management System . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 4.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86 5 Personal Music Knowledge Base in Practice 87 5.1 Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 5.1.1 AudioScrobbler RDF Service . . . . . . . . . . . . . . . . . . . . . . . . . . 87 5.1.2 PMKB ID3 Tag Extractor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 5.2 Evaluation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 5.2.1 Reutilisation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90 5.2.2 Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 5.2.3 Reviews and Mentions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 5.2.4 Indexing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91 5.3 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92 6 Conclusion and Future Work 93 6.1 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93 6.2 Future Work . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

Creation and extension of ontologies for describing communications in the context of organizations

Thesis submitted to Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa, in partial fulfillment of the requirements for the degree of Master in Computer ScienceThe use of ontologies is nowadays a sufficiently mature and solid field of work to be considered an efficient alternative in knowledge representation. With the crescent growth of the Semantic Web, it is expectable that this alternative tends to emerge even more in the near future. In the context of a collaboration established between FCT-UNL and the R&D department of a national software company, a new solution entitled ECC – Enterprise Communications Center was developed. This application provides a solution to manage the communications that enter, leave or are made within an organization, and includes intelligent classification of communications and conceptual search techniques in a communications repository. As specificity may be the key to obtain acceptable results with these processes, the use of ontologies becomes crucial to represent the existing knowledge about the specific domain of an organization. This work allowed us to guarantee a core set of ontologies that have the power of expressing the general context of the communications made in an organization, and of a methodology based upon a series of concrete steps that provides an effective capability of extending the ontologies to any business domain. By applying these steps, the minimization of the conceptualization and setup effort in new organizations and business domains is guaranteed. The adequacy of the core set of ontologies chosen and of the methodology specified is demonstrated in this thesis by its effective application to a real case-study, which allowed us to work with the different types of sources considered in the methodology and the activities that support its construction and evolution