Digital Preservation, Archival Science and Methodological Foundations for Digital Libraries

Digital libraries, whether commercial, public or personal, lie at the heart of the information society. Yet, research into their long‐term viability and the meaningful accessibility of their contents remains in its infancy. In general, as we have pointed out elsewhere, ‘after more than twenty years of research in digital curation and preservation the actual theories, methods and technologies that can either foster or ensure digital longevity remain startlingly limited.’ Research led by DigitalPreservationEurope (DPE) and the Digital Preservation Cluster of DELOS has allowed us to refine the key research challenges – theoretical, methodological and technological – that need attention by researchers in digital libraries during the coming five to ten years, if we are to ensure that the materials held in our emerging digital libraries are to remain sustainable, authentic, accessible and understandable over time. Building on this work and taking the theoretical framework of archival science as bedrock, this paper investigates digital preservation and its foundational role if digital libraries are to have long‐term viability at the centre of the global information society.

AdSchema : a schema for semistructured data

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The IUPHAR/BPS Guide to PHARMACOLOGY in 2016: towards curated quantitative interactions between 1300 protein targets and 6000 ligands

The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, http://www.guidetopharmacology.org) provides expert-curated molecular interactions between successful and potential drugs and their targets in the human genome. Developed by the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS), this resource, and its earlier incarnation as IUPHAR-DB, is described in our 2014 publication. This update incorporates changes over the intervening seven database releases. The unique model of content capture is based on established and new target class subcommittees collaborating with in-house curators. Most information comes from journal articles, but we now also index kinase cross-screening panels. Targets are specified by UniProtKB IDs. Small molecules are defined by PubChem Compound Identifiers (CIDs); ligand capture also includes peptides and clinical antibodies. We have extended the capture of ligands and targets linked via published quantitative binding data (e.g. Ki, IC50 or Kd). The resulting pharmacological relationship network now defines a data-supported druggable genome encompassing 7% of human proteins. The database also provides an expanded substrate for the biennially published compendium, the Concise Guide to PHARMACOLOGY. This article covers content increase, entity analysis, revised curation strategies, new website features and expanded download options

The Mixed Powerdomain

This paper introduces an operator M called the mixed powerdomain which generalizes the convex (Plotkin) powerdomain. The construction is based on the idea of representing partial information about a set of data items using a pair of sets, one representing partial information in the manner of the upper (Smyth) powerdomain and the other in the manner of the lower (Hoare) powerdomain where the components of such pairs are required to satisfy a consistency condition. This provides a richer family of meaningful partial descriptions than are available in the convex powerdomain and also makes it possible to include the empty set in a satisfactory way. The new construct is given a rigorous mathematical treatment like that which has been applied to the known powerdomains. It is proved that M is a continuous functor on bifinite domains which is left adjoint to the forgetful functor from a category of continuous structures called mix algebras. For a domain D with a coherent Scott topology, elements of M D can be represented as pairs (U, V) where U ⊆ D is a compact upper set, V ⊆ D is a closed set and the downward closure of U ∩ V is equal to V. A Stone dual characterization of M is also provided

Development of Use Cases, Part I

For determining requirements and constructs appropriate for a Web query language, or in fact any language, use cases are of essence. The W3C has published two sets of use cases for XML and RDF query languages. In this article, solutions for these use cases are presented using Xcerpt. a novel Web and Semantic Web query language that combines access to standard Web data such as XML documents with access to Semantic Web metadata such as RDF resource descriptions with reasoning abilities and rules familiar from logicprogramming. To the best knowledge of the authors, this is the first in depth study of how to solve use cases for accessing XML and RDF in a single language: Integrated access to data and metadata has been recognized by industry and academia as one of the key challenges in data processing for the next decade. This article is a contribution towards addressing this challenge by demonstrating along practical and recognized use cases the usefulness of reasoning abilities, rules, and semistructured query languages for accessing both data (XML) and metadata (RDF)