How much is involved in DB publishing?

XML has been intensive investigated lately, with the sentence, that "XML is (has been) the standard form for data publishing", especially in data base area.That is, there are assumptions, that the newly published data take mostly the form of XML documents, particularly when databases are involved. This presumption seems to be the reason of the heavy investment applied for researching the topics of handling, querying and comprising XML documents. We check these assumptions by investigating the documents accessible on the Internet, possible going under the surface, into the "deep Web". The investigation involves analyzing large scientific databases, but the commercial data stored in the "deep Web" will be handled also.We used the technique of randomly generated IP addresses for investigating the "deep Web", i.e. the part of the Internet not indexed by the search engines. For the part of the Web that is accessed (indexed) by the large search engines we used the random walk technique to collect uniformly distributed samplings. We found, that XML has not(yet) been the standard of Web publishing, but it is strongly represented on the Web. We add a simple new evaluation method to the known uniformly sampling processes.These investigations can be repeated in the future in order to get a dynamic picture of the growing rate of the number of the XML documents present on the Web

Encoding models for scholarly literature

We examine the issue of digital formats for document encoding, archiving and publishing, through the specific example of "born-digital" scholarly journal articles. We will begin by looking at the traditional workflow of journal editing and publication, and how these practices have made the transition into the online domain. We will examine the range of different file formats in which electronic articles are currently stored and published. We will argue strongly that, despite the prevalence of binary and proprietary formats such as PDF and MS Word, XML is a far superior encoding choice for journal articles. Next, we look at the range of XML document structures (DTDs, Schemas) which are in common use for encoding journal articles, and consider some of their strengths and weaknesses. We will suggest that, despite the existence of specialized schemas intended specifically for journal articles (such as NLM), and more broadly-used publication-oriented schemas such as DocBook, there are strong arguments in favour of developing a subset or customization of the Text Encoding Initiative (TEI) schema for the purpose of journal-article encoding; TEI is already in use in a number of journal publication projects, and the scale and precision of the TEI tagset makes it particularly appropriate for encoding scholarly articles. We will outline the document structure of a TEI-encoded journal article, and look in detail at suggested markup patterns for specific features of journal articles

Introducing Texture: An Open Source WYSIWYG Javascript Editor for JATS

Texture is a WYSIWYG editor app that allows users to turn raw content into structured content, and add as much semantic information as needed for the production of scientific publications. Texture is open source software built on top of Substance (http://substance.io), an advanced Javascript content authoring library. While the Substance library is format agnostic, the Texture editor uses JATS XML as a native exchange format. The Substance library that Texture is built on already supports real-time collaborative authoring, and the easy-to-use WYSIWYG interface would make Texture an attractive alternative to Google Docs. For some editors, the interface could be toggled to more closely resemble a professional XML suite, allowing a user to pop out a raw attribute editor for any given element. Textureauthored documents could then be brought into the journal management system directly, skipping the conversion step, and move straight into a document-centric publishing workflow. &nbsp

SCOPE - A Scientific Compound Object Publishing and Editing System

This paper presents the SCOPE (Scientific Compound Object Publishing and Editing) system which is designed to enable scientists to easily author, publish and edit scientific compound objects. Scientific compound objects enable scientists to encapsulate the various datasets and resources generated or utilized during a scientific experiment or discovery process, within a single compound object, for publishing and exchange. The adoption of “named graphs” to represent these compound objects enables provenance information to be captured via the typed relationships between the components. This approach is also endorsed by the OAI-ORE initiative and hence ensures that we generate OAI-ORE-compliant Scientific Compound Objects. The SCOPE system is an extension of the Provenance Explorer tool – which enables access-controlled viewing of scientific provenance trails. Provenance Explorer provided dynamic rendering of RDF graphs of scientific discovery processes, showing the lineage from raw data to publication. Views of different granularity can be inferred automatically using SWRL (Semantic Web Rules Language) rules and an inferencing engine. SCOPE extends the Provenance Explorer tool and GUI by: 1) Adding an embedded web browser that can be used for incorporating objects discoverable via the Web; 2) Representing compound objects as Named Graphs, that can be saved in RDF, TriX, TriG or as an Atom syndication feed; 3) Enabling scientists to attach Creative Commons Licenses to the compound objects to specify how they may be re-used; 4) Enabling compound objects to be published as Fedora Object XML (FOXML) files within a Fedora digital library

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

Fast, linked, and open – the future of taxonomic publishing for plants: launching the journal PhytoKeys

The paper describes the focus, scope and the rationale of PhytoKeys, a newly established, peer-reviewed, open-access journal in plant systematics. PhytoKeys is launched to respond to four main challenges of our time: (1) Appearance of electronic publications as amendments or even alternatives to paper publications; (2) Open Access (OA) as a new publishing model; (3) Linkage of electronic registers, indices and aggregators that summarize information on biological species through taxonomic names or their persistent identifiers (Globally Unique Identifiers or GUIDs; currently Life Science Identifiers or LSIDs); (4) Web 2.0 technologies that permit the semantic markup of, and semantic enhancements to, published biological texts. The journal will pursue cutting-edge technologies in publication and dissemination of biodiversity information while strictly following the requirements of the current International Code of Botanical Nomenclature (ICBN)

EJT editorial standard for the semantic enhancement of specimen data in taxonomy literature

This paper describes a set of guidelines for the citation of zoological and botanical specimens in the European Journal of Taxonomy. The guidelines stipulate controlled vocabularies and precise formats for presenting the specimens examined within a taxonomic publication, which allow for the rich data associated with the primary research material to be harvested, distributed and interlinked online via international biodiversity data aggregators. Herein we explain how the EJT editorial standard was defined and how this initiative fits into the journal's project to semantically enhance its publications using the Plazi TaxPub DTD extension. By establishing a standardised format for the citation of taxonomic specimens, the journal intends to widen the distribution of and improve accessibility to the data it publishes. Authors who conform to these guidelines will benefit from higher visibility and new ways of visualising their work. In a wider context, we hope that other taxonomy journals will adopt this approach to their publications, adapting their working methods to enable domain-specific text mining to take place. If specimen data can be efficiently cited, harvested and linked to wider resources, we propose that there is also the potential to develop alternative metrics for assessing impact and productivity within the natural science

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