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)

Three Steps to Heaven: Semantic Publishing in a Real World Workflow

Semantic publishing offers the promise of computable papers, enriched visualisation and a realisation of the linked data ideal. In reality, however, the publication process contrives to prevent richer semantics while culminating in a `lumpen' PDF. In this paper, we discuss a web-first approach to publication, and describe a three-tiered approach which integrates with the existing authoring tooling. Critically, although it adds limited semantics, it does provide value to all the participants in the process: the author, the reader and the machine.Comment: Published as part of SePublica 201

Wikis in scholarly publishing

Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on "Species-ID":http://species-id.net/w/index.php?title=Wikis_in_scholarly_publishing&oldid=3815 - a wiki that hosts a prototype for wiki-based scholarly publishing - where it can be updated, expanded or otherwise improved

Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article

Scientific innovation depends on finding, integrating, and re-using the products of previous research. Here we explore how recent developments in Web technology, particularly those related to the publication of data and metadata, might assist that process by providing semantic enhancements to journal articles within the mainstream process of scholarly journal publishing. We exemplify this by describing semantic enhancements we have made to a recent biomedical research article taken from PLoS Neglected Tropical Diseases, providing enrichment to its content and increased access to datasets within it. These semantic enhancements include provision of live DOIs and hyperlinks; semantic markup of textual terms, with links to relevant third-party information resources; interactive figures; a re-orderable reference list; a document summary containing a study summary, a tag cloud, and a citation analysis; and two novel types of semantic enrichment: the first, a Supporting Claims Tooltip to permit “Citations in Context”, and the second, Tag Trees that bring together semantically related terms. In addition, we have published downloadable spreadsheets containing data from within tables and figures, have enriched these with provenance information, and have demonstrated various types of data fusion (mashups) with results from other research articles and with Google Maps. We have also published machine-readable RDF metadata both about the article and about the references it cites, for which we developed a Citation Typing Ontology, CiTO (http://purl.org/net/cito/). The enhanced article, which is available at http://dx.doi.org/10.1371/journal.pntd.0000228.x001, presents a compelling existence proof of the possibilities of semantic publication. We hope the showcase of examples and ideas it contains, described in this paper, will excite the imaginations of researchers and publishers, stimulating them to explore the possibilities of semantic publishing for their own research articles, and thereby break down present barriers to the discovery and re-use of information within traditional modes of scholarly communication

One document, many users: what happens when you re-purpose a document?

To assess global challenges surrounding issues such as climate change and invasive species requires a baseline of historical data. We are fortunate in biodiversity that such data exists in a rich body of literature. One such source of historical data is the Biologia Centrali-Americana (BCA), which documents the plant and animal life in Central America one hundred years’ ago, and which can be compared to contemporary species distributions. This valuable resource has recently been re-keyed and manually marked up by the INOTAXA project (http://www.inotaxa.org/). The 56-volume work is now being curated before wider release. The manual annotation of the BCA is both time consuming in its initial phases and demands expert review to curate the results. This manual approach to mining historic texts is not viable for large-scale works such as the BCA. Attempts to automate the process face the problem of not having suitable corpora against which to develop and then test automated solutions such as text mining. One project, ViBRANT (http://vbrant.eu/), sought to use the scale of the re-keyed data being produced by INOTAXA to develop a solution to this problem. However, this apparently straightforward task has thrown up many issues because different audiences have different requirements of the mark up. This presentation describes the process by which the BCA is being reworked from digitisation through to a curated document corpus. The intended users are biodiversity scientists who can use the corpus for taxonomic and biodiversity research, and computer scientists who can use it to develop new text mining and mark up tools. The presentation covers the different requirements of scientists in the two domains, how this affects the mark up required of the documents, and how to re-purpose the annotations to meet the needs of different and sometimes disparate scientific audiences

Wikipedia-Based Semantic Enhancements for Information Nugget Retrieval

When the objective of an information retrieval task is to return a nugget rather than a document, query terms that exist in a document often will not be used in the most relevant nugget in the document for the query. In this thesis a new method of query expansion is proposed based on the Wikipedia link structure surrounding the most relevant articles selected either automatically or by human assessors for the query. Evaluated with the Nuggeteer automatic scoring software, which we show to have a high correlation with human assessor scores for the ciQA 2006 topics, an increase in the F-scores is found from the TREC Complex Interactive Question Answering task when integrating this expansion into an already high-performing baseline system. In addition, the method for finding synonyms using Wikipedia is evaluated using more common synonym detection tasks

Quality-aware model-driven service engineering

Service engineering and service-oriented architecture as an integration and platform technology is a recent approach to software systems integration. Quality aspects ranging from interoperability to maintainability to performance are of central importance for the integration of heterogeneous, distributed service-based systems. Architecture models can substantially influence quality attributes of the implemented software systems. Besides the benefits of explicit architectures on maintainability and reuse, architectural constraints such as styles, reference architectures and architectural patterns can influence observable software properties such as performance. Empirical performance evaluation is a process of measuring and evaluating the performance of implemented software. We present an approach for addressing the quality of services and service-based systems at the model-level in the context of model-driven service engineering. The focus on architecture-level models is a consequence of the black-box character of services

Web Service Discovery in the FUSION Semantic Registry

The UDDI specification was developed as an attempt to address the key challenge of effective Web service discovery and has become a widely adopted standard. However, the text-based indexing and search mechanism that UDDI registries offer does not suffice for expressing unambiguous and semantically rich representations of service capabilities, and cannot support the logic-based inference capacity required for facilitating automated service matchmaking. This paper provides an overview of the approach put forward in the FUSION project for overcoming this important limitation. Our solution combines SAWSDL-based service descriptions with service capability profiling based on OWL-DL, and automated matchmaking through DL reasoning in a semantically extended UDDI registry