Object linking in repositories

This topic is covered in three sections. The first section explores some of the architectural ramifications of extending the Eichmann/Atkins lattice-based classification scheme to encompass the assets of the full life cycle of software development. A model is considered that provides explicit links between objects in addition to the edges connecting classification vertices in the standard lattice. The second section gives a description of the efforts to implement the repository architecture using a commercially available object-oriented database management system. Some of the features of this implementation are described, and some of the next steps to be taken to produce a working prototype of the repository are pointed out. In the final section, it is argued that design and instantiation of reusable components have competing criteria (design-for-reuse strives for generality, design-with-reuse strives for specificity) and that providing mechanisms for each can be complementary rather than antagonistic. In particular, it is demonstrated how program slicing techniques can be applied to customization of reusable components

A cooperative-relational approach to digital libraries

Copyright @ 2007 Springer-Verlag, Berlin HeidelbergThis paper presents a novel approach to model-driven development of Digital Library (DL) systems. The overall idea is to allow Digital Library systems designers (e.g. information architects, librarians, domain experts) to easily design such systems by using a visual language. We designed a Domain Specific Visual Language for such a purpose and developed a framework supporting it; this framework helps designers by automatically generating code for the defined Digital Library system, so that they do not have to get involved into technical issues concerning its deployment. In our approach, both Human-Computer Interaction and Computer Supported Collaborative Work techniques are exploited when generating interfaces and services for the specific Digital Library domain

Annotating digital libraries and electronic editions in a collaborative and semantic perspective

The distinction between digital libraries and electronic editions is becom-ing more and more subtle. The practice of annotation represents a point of conver-gence of two only apparently separated worlds. The aim of this paper is to present a model of collaborative semantic annotation of texts (SemLib project), suggesting a system that find in Semantic Web and Linked Data the solution technologies for en-abling structured semantic annotation, also in the field of electronic editions in Digi-tal Humanities domain. The main purpose of SemLib is to develop an application so to make easy for developers the integration of annotation software in digital librar-ies, which are different both for technical implementations and managed contents, and provide to users, indifferently from their cultural backgrounds, a simple system which could be used as a front-end. We present, for this purpose, a final example of semantic annotation in a specific context: a digital edition of a literary text and the issues that an annotation task involves

Linking Textual Resources to Support Information Discovery

A vast amount of information is today stored in the form of textual documents, many of which are available online. These documents come from different sources and are of different types. They include newspaper articles, books, corporate reports, encyclopedia entries and research papers. At a semantic level, these documents contain knowledge, which was created by explicitly connecting information and expressing it in the form of a natural language. However, a significant amount of knowledge is not explicitly stated in a single document, yet can be derived or discovered by researching, i.e. accessing, comparing, contrasting and analysing, information from multiple documents. Carrying out this work using traditional search interfaces is tedious due to information overload and the difficulty of formulating queries that would help us to discover information we are not aware of. In order to support this exploratory process, we need to be able to effectively navigate between related pieces of information across documents. While information can be connected using manually curated cross-document links, this approach not only does not scale, but cannot systematically assist us in the discovery of sometimes non-obvious (hidden) relationships. Consequently, there is a need for automatic approaches to link discovery. This work studies how people link content, investigates the properties of different link types, presents new methods for automatic link discovery and designs a system in which link discovery is applied on a collection of millions of documents to improve access to public knowledge

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

Sharing Cultural Heritage: the Clavius on the Web Project

In the last few years the amount of manuscripts digitized and made available on the Web has been constantly increasing. However, there is still a considarable lack of results concerning both the explicitation of their content and the tools developed to make it available. The objective of the Clavius on the Web project is to develop a Web platform exposing a selection of Christophorus Clavius letters along with three different levels of analysis: linguistic, lexical and semantic. The multilayered annotation of the corpus involves a XML-TEI encoding followed by a tokenization step where each token is univocally identified through a CTS urn notation and then associated to a part-of-speech and a lemma. The text is lexically and semantically annotated on the basis of a lexicon and a domain ontology, the former structuring the most relevant terms occurring in the text and the latter representing the domain entities of interest (e.g. people, places, etc.). Moreover, each entity is connected to linked and non linked resources, including DBpedia and VIAF. Finally, the results of the three layers of analysis are gathered and shown through interactive visualization and storytelling techniques. A demo version of the integrated architecture was developed

AI driven B-cell Immunotherapy Design

Antibodies, a prominent class of approved biologics, play a crucial role in detecting foreign antigens. The effectiveness of antigen neutralisation and elimination hinges upon the strength, sensitivity, and specificity of the paratope-epitope interaction, which demands resource-intensive experimental techniques for characterisation. In recent years, artificial intelligence and machine learning methods have made significant strides, revolutionising the prediction of protein structures and their complexes. The past decade has also witnessed the evolution of computational approaches aiming to support immunotherapy design. This review focuses on the progress of machine learning-based tools and their frameworks in the domain of B-cell immunotherapy design, encompassing linear and conformational epitope prediction, paratope prediction, and antibody design. We mapped the most commonly used data sources, evaluation metrics, and method availability and thoroughly assessed their significance and limitations, discussing the main challenges ahead

Safe to Be Open: Study on the Protection of Research Data and Recommendations for Access and Usage

Openness has become a common concept in a growing number of scientific and academic fields. Expressions such as Open Access (OA) or Open Content (OC) are often employed for publications of papers and research results, or are contained as conditions in tenders issued by a number of funding agencies. More recently the concept of Open Data (OD) is of growing interest in some fields, particularly those that produce large amounts of data – which are not usually protected by standard legal tools such as copyright. However, a thorough understanding of the meaning of Openness – especially its legal implications – is usually lacking. Open Access, Public Access, Open Content, Open Data, Public Domain. All these terms are often employed to indicate that a given paper, repository or database does not fall under the traditional “closed” scheme of default copyright rules. However, the differences between all these terms are often largely ignored or misrepresented, especially when the scientist in question is not familiar with the law generally and copyright in particular – a very common situation in all scientific fields. On 17 July 2012 the European Commission published its Communication to the European Parliament and the Council entitled “Towards better access to scientific information: Boosting the benefits of public investments in research”. As the Commission observes, “discussions of the scientific dissemination system have traditionally focused on access to scientific publications – journals and monographs. However, it is becoming increasingly important to improve access to research data (experimental results, observations and computer-generated information), which forms the basis for the quantitative analysis underpinning many scientific publications”. The Commission believes that through more complete and wider access to scientific publications and data, the pace of innovation will accelerate and researchers will collaborate so that duplication of efforts will be avoided. Moreover, open research data will allow other researchers to build on previous research results, as it will allow involvement of citizens and society in the scientific process. In the Communication the Commission makes explicit reference to open access models of publications and dissemination of research results, and the reference is not only to access and use but most significantly to reuse of publications as well as research data. The Communication marks an official new step on the road to open access to publicly funded research results in science and the humanities in Europe. Scientific publications are no longer the only elements of its open access policy: research data upon which publications are based should now also be made available to the public. As noble as the open access goal is, however, the expansion of the open access policy to publicly funded research data raises a number of legal and policy issues that are often distinct from those concerning the publication of scientific articles and monographs. Since open access to research data – rather than publications – is a relatively new policy objective, less attention has been paid to the specific features of research data. An analysis of the legal status of such data, and on how to make it available under the correct licence terms, is therefore the subject of the following sections