The NASA Astrophysics Data System: Data Holdings

Since its inception in 1993, the ADS Abstract Service has become an indispensable research tool for astronomers and astrophysicists worldwide. In those seven years, much effort has been directed toward improving both the quantity and the quality of references in the database. From the original database of approximately 160,000 astronomy abstracts, our dataset has grown almost tenfold to approximately 1.5 million references covering astronomy, astrophysics, planetary sciences, physics, optics, and engineering. We collect and standardize data from approximately 200 journals and present the resulting information in a uniform, coherent manner. With the cooperation of journal publishers worldwide, we have been able to place scans of full journal articles on-line back to the first volumes of many astronomical journals, and we are able to link to current version of articles, abstracts, and datasets for essentially all of the current astronomy literature. The trend toward electronic publishing in the field, the use of electronic submission of abstracts for journal articles and conference proceedings, and the increasingly prominent use of the World Wide Web to disseminate information have enabled the ADS to build a database unparalleled in other disciplines. The ADS can be accessed at http://adswww.harvard.eduComment: 24 pages, 1 figure, 6 tables, 3 appendice

Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

Novel metabolites distinct from canonical pathways can be identified through the integration of three cheminformatics tools: BinVestigate, which queries the BinBase gas chromatography-mass spectrometry (GC-MS) metabolome database to match unknowns with biological metadata across over 110,000 samples; MS-DIAL 2.0, a software tool for chromatographic deconvolution of high-resolution GC-MS or liquid chromatography-mass spectrometry (LC-MS); and MS-FINDER 2.0, a structure-elucidation program that uses a combination of 14 metabolome databases in addition to an enzyme promiscuity library. We showcase our workflow by annotating N-methyl-uridine monophosphate (UMP), lysomonogalactosyl-monopalmitin, N-methylalanine, and two propofol derivatives

Digital Preservation Services : State of the Art Analysis

Research report funded by the DC-NET project.An overview of the state of the art in service provision for digital preservation and curation. Its focus is on the areas where bridging the gaps is needed between e-Infrastructures and efficient and forward-looking digital preservation services. Based on a desktop study and a rapid analysis of some 190 currently available tools and services for digital preservation, the deliverable provides a high-level view on the range of instruments currently on offer to support various functions within a preservation system.European Commission, FP7peer-reviewe

Theory and Practice of Data Citation

Citations are the cornerstone of knowledge propagation and the primary means of assessing the quality of research, as well as directing investments in science. Science is increasingly becoming "data-intensive", where large volumes of data are collected and analyzed to discover complex patterns through simulations and experiments, and most scientific reference works have been replaced by online curated datasets. Yet, given a dataset, there is no quantitative, consistent and established way of knowing how it has been used over time, who contributed to its curation, what results have been yielded or what value it has. The development of a theory and practice of data citation is fundamental for considering data as first-class research objects with the same relevance and centrality of traditional scientific products. Many works in recent years have discussed data citation from different viewpoints: illustrating why data citation is needed, defining the principles and outlining recommendations for data citation systems, and providing computational methods for addressing specific issues of data citation. The current panorama is many-faceted and an overall view that brings together diverse aspects of this topic is still missing. Therefore, this paper aims to describe the lay of the land for data citation, both from the theoretical (the why and what) and the practical (the how) angle.Comment: 24 pages, 2 tables, pre-print accepted in Journal of the Association for Information Science and Technology (JASIST), 201

Image database system for glaucoma diagnosis support

Tato práce popisuje přehled standardních a pokročilých metod používaných k diagnose glaukomu v ranném stádiu. Na základě teoretických poznatků je implementován internetově orientovaný informační systém pro oční lékaře, který má tři hlavní cíle. Prvním cílem je možnost sdílení osobních dat konkrétního pacienta bez nutnosti posílat tato data internetem. Druhým cílem je vytvořit účet pacienta založený na kompletním očním vyšetření. Posledním cílem je aplikovat algoritmus pro registraci intenzitního a barevného fundus obrazu a na jeho základě vytvořit internetově orientovanou tři-dimenzionální vizualizaci optického disku. Tato práce je součásti DAAD spolupráce mezi Ústavem Biomedicínského Inženýrství, Vysokého Učení Technického v Brně, Oční klinikou v Erlangenu a Ústavem Informačních Technologií, Friedrich-Alexander University, Erlangen-Nurnberg.This master thesis describes a conception of standard and advanced eye examination methods used for glaucoma diagnosis in its early stage. According to the theoretical knowledge, a web based information system for ophthalmologists with three main aims is implemented. The first aim is the possibility to share medical data of a concrete patient without sending his personal data through the Internet. The second aim is to create a patient account based on a complete eye examination procedure. The last aim is to improve the HRT diagnostic method with an image registration algorithm for the fundus and intensity images and create an optic nerve head web based 3D visualization. This master thesis is a part of project based on DAAD co-operation between Department of Biomedical Engineering, Brno University of Technology, Eye Clinic in Erlangen and Department of Computer Science, Friedrich-Alexander University, Erlangen-Nurnberg.

MoPark Initiative, Metadata Options Appraisal (Phase I)

Examines – and makes recommendations on - the needs of the Loch Lomond and Trossachs National Park as regards the metadata, metadata standards, and metadata management required for the competent handling of digital materials both now and in the future. Proposes an iterative approach to determining metadata requirements, working within a METS-based framework

File-based storage of Digital Objects and constituent datastreams: XMLtapes and Internet Archive ARC files

This paper introduces the write-once/read-many XMLtape/ARC storage approach for Digital Objects and their constituent datastreams. The approach combines two interconnected file-based storage mechanisms that are made accessible in a protocol-based manner. First, XML-based representations of multiple Digital Objects are concatenated into a single file named an XMLtape. An XMLtape is a valid XML file; its format definition is independent of the choice of the XML-based complex object format by which Digital Objects are represented. The creation of indexes for both the identifier and the creation datetime of the XML-based representation of the Digital Objects facilitates OAI-PMH-based access to Digital Objects stored in an XMLtape. Second, ARC files, as introduced by the Internet Archive, are used to contain the constituent datastreams of the Digital Objects in a concatenated manner. An index for the identifier of the datastream facilitates OpenURL-based access to an ARC file. The interconnection between XMLtapes and ARC files is provided by conveying the identifiers of ARC files associated with an XMLtape as administrative information in the XMLtape, and by including OpenURL references to constituent datastreams of a Digital Object in the XML-based representation of that Digital Object.Comment: 12 pages, 1 figures (camera-ready copy for ECDL 2005

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