Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

BlogForever: D3.1 Preservation Strategy Report

This report describes preservation planning approaches and strategies recommended by the BlogForever project as a core component of a weblog repository design. More specifically, we start by discussing why we would want to preserve weblogs in the first place and what it is exactly that we are trying to preserve. We further present a review of past and present work and highlight why current practices in web archiving do not address the needs of weblog preservation adequately. We make three distinctive contributions in this volume: a) we propose transferable practical workflows for applying a combination of established metadata and repository standards in developing a weblog repository, b) we provide an automated approach to identifying significant properties of weblog content that uses the notion of communities and how this affects previous strategies, c) we propose a sustainability plan that draws upon community knowledge through innovative repository design

In search of comity: TEI for distant reading

Any expansion of the TEI beyond its traditional user base involves a recognition that there are many differing answers to the traditional question “What is text, really?” We report on some work carried out in the context of the COST Action Distant Reading for European Literary History (CA16204), in particular on the TEI-conformant schemas developed for one of its principal deliverables: the European Literary Text Collection (ELTeC). The ELTeC will contain comparable corpora for each of at least a dozen European languages, each being a balanced sample of one hundred novels from the period 1840 to 1920, together with metadata concerning their production and reception. We hope that it will become a reliable basis for comparative work in data-driven textual analytics. The focus of the ELTeC encoding scheme is not to represent texts in all their original complexity, nor to duplicate the work of scholarly editors. Instead, we aim to facilitate a richer and better-informed distant reading than a transcription of lexical content alone would permit. At the same time, where the TEI encourages diversity, we enforce consistency by permitting representation of only a specific and quite small set of textual features, both structural and analytical. These constraints are expressed by a master TEI ODD, from which we derive three different schemas by ODD chaining, each associated with appropriate documentation

Strategies for Sustaining Digital Libraries

This collection of essays is a report of early findings from pioneers who have worked to establishdigital libraries, not merely as experimental projects, but as ongoing services and collectionsintended to be sustained over time in ways consistent with the long-held practices of print-basedlibraries. Particularly during this period of extreme technological transition, it is imperative thatprograms across the nation – and indeed the world – actively share their innovations,experiences, and techniques in order to begin cultivating new isomorphic, or commonly held,practices. The collective sentiment of the field is that we must begin to transition from apunctuated, project-based mode of advancing innovative information services to an ongoingprogrammatic mode of sustaining digital libraries for the long haul

Development of linguistic linked open data resources for collaborative data-intensive research in the language sciences

Making diverse data in linguistics and the language sciences open, distributed, and accessible: perspectives from language/language acquistiion researchers and technical LOD (linked open data) researchers. This volume examines the challenges inherent in making diverse data in linguistics and the language sciences open, distributed, integrated, and accessible, thus fostering wide data sharing and collaboration. It is unique in integrating the perspectives of language researchers and technical LOD (linked open data) researchers. Reporting on both active research needs in the field of language acquisition and technical advances in the development of data interoperability, the book demonstrates the advantages of an international infrastructure for scholarship in the field of language sciences. With contributions by researchers who produce complex data content and scholars involved in both the technology and the conceptual foundations of LLOD (linguistics linked open data), the book focuses on the area of language acquisition because it involves complex and diverse data sets, cross-linguistic analyses, and urgent collaborative research. The contributors discuss a variety of research methods, resources, and infrastructures. Contributors Isabelle Barrière, Nan Bernstein Ratner, Steven Bird, Maria Blume, Ted Caldwell, Christian Chiarcos, Cristina Dye, Suzanne Flynn, Claire Foley, Nancy Ide, Carissa Kang, D. Terence Langendoen, Barbara Lust, Brian MacWhinney, Jonathan Masci, Steven Moran, Antonio Pareja-Lora, Jim Reidy, Oya Y. Rieger, Gary F. Simons, Thorsten Trippel, Kara Warburton, Sue Ellen Wright, Claus Zin

Expert knowledge management based on ontology in a digital library

The architecture of the future Digital Libraries should be able to allow any users to access available knowledge resources from anywhere and at any time and efficient manner. Moreover to the individual user, there is a great deal of useless information in addition to the substantial amount of useful information. The goal is to investigate how to best combine Artificial Intelligent and Semantic Web technologies for semantic searching across largely distributed and heterogeneous digital libraries. The Artificial Intelligent and Semantic Web have provided both new possibilities and challenges to automatic information processing in search engine process. The major research tasks involved are to apply appropriate infrastructure for specific digital library system construction, to enrich metadata records with ontologies and enable semantic searching upon such intelligent system infrastructure. We study improving the efficiency of search methods to search a distributed data space like a Digital Library. This paper outlines the development of a CaseBased Reasoning prototype system based in an ontology for retrieval information of the Digital Library University of Seville. The results demonstrate that the used of expert system and the ontology into the retrieval process, the effectiveness of the information retrieval is enhanced

Development of Linguistic Linked Open Data Resources for Collaborative Data-Intensive Research in the Language Sciences

This book is the product of an international workshop dedicated to addressing data accessibility in the linguistics field. It is therefore vital to the book’s mission that its content be open access. Linguistics as a field remains behind many others as far as data management and accessibility strategies. The problem is particularly acute in the subfield of language acquisition, where international linguistic sound files are needed for reference. Linguists' concerns are very much tied to amount of information accumulated by individual researchers over the years that remains fragmented and inaccessible to the larger community. These concerns are shared by other fields, but linguistics to date has seen few efforts at addressing them. This collection, undertaken by a range of leading experts in the field, represents a big step forward. Its international scope and interdisciplinary combination of scholars/librarians/data consultants will provide an important contribution to the field

That obscure object of desire: multimedia metadata on the Web, part 1

This article discusses the state of the art in metadata for audio-visual media in large semantic networks, such as the Semantic Web. Our discussion is predominantly motivated by the two most widely known approaches towards machine-processable and semantic-based content description, namely the Semantic Web activity of the W3C and ISO's efforts in the direction of complex media content modeling, in particular the Multimedia Content Description Interface (MPEG-7). We explain that the conceptual ideas and technologies discussed in both approaches are essential for the next step in multim