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

Abstract

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.

Semantic publishing: the coming revolution in scientific journal publishing

“…Disappointingly, these tabs are presently limited to ' Abstract', 'Article' and 'References', with no breakdown of the article into Introduction, Methods, Results, etc., and these tabs scroll out of sight when reading down the page. The equivalent sectional functionality provided by the non-scrolling link set at the top of the enhanced PLoS Neglected Tropical Diseases article (http://dx.doi.org/10.1371/ journal.pntd.0000228.x001) described by Shotton et al, 5 and discussed below, provides much better functionality while occupying less screen real-estate.…”

“…In Shotton et al 5 we describe the semantic enhancements that we have made to a recent article by Reis et al 10 We created a document summary containing document statistics; a study summary, a tag Semantic publishing: the coming revolution in scientific journal publishing 89…”

Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles

“…Last but not least, using a controlled subset of HTML is more appropriate for Semantic Publishing applications (Shotton et al, 2009;Peroni, 2014b). The development of scripts and applications to extract, for instance, RDF statements directly from the markup structure of the text is a sort of nightmare if different authors use HTML in different manners.…”

“…Besides the obvious justification of simplification and unification of data formats for drafting, submission and publication, an additional underlying rationale is that the adoption of HTML would ease the embedding of semantic annotations, thus improving research communications thanks to already existing W3C standards such as RDFa (Sporny, 2015), Turtle (Prud'hommeaux & Carothers, 2014) and JSON-LD (Sporny, Kellogg & Lanthaler, 2014). This opens complex and exciting scenarios that the Semantic Publishing community has promised us in terms of increased discoverability, interactivity, openness and usability of the scientific works (Bourne et al, 2011;Shotton et al, 2009).…”

A Linked-Data-Driven and Semantically-Enabled Journal Portal for Scientometrics

“…To semantically disambiguate the bibliographic vocabularies, researchers have developed a number of bibliographic ontologies to annotate and structure their data [7]. BIBO is one of these bibliographic ontologies.…”