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Tag: standards

Nomenclature for citations and references

Reis et al. (2008) [1] cites an earlier paper from Albert Ko’s research group, Ko et al. (1999) [2].

In conventional parlance, as the following diagram shows, the word “reference” can mean either what is found in the text, what is found in the reference list, the act of citation, or the object of the citation itself, as in the sentence “All the references you will need to prepare for the journal club are on Kevin’s desk”.

This situation does not make for unambiguous machine-readable encoding, so to improve the situation we have, in the SPAR (Semantic Publishing and Referencing) Ontologies, introduced a more principled way of referring to these items and actions, as the second diagram illustrates:

This permits us to create RDF describing all aspect of the citation process. Within the body of the text we have an in-text citation containing an in-text reference pointer, while the actual bibliographic reference that the in-text reference pointer denotes is to be found within the article’s reference list. That bibliographic reference references the cited article, while the whole performative act of including the reference in the article constitutes the act of citation.

Are we all clear now?

[1] Reis RB, Ribeiro GS, Felzemburgh RDM, Santana FS, Mohr S, Melendez AXTO, Queiroz A, Santos AC, Ravines RR, Tassinari WS, Carvalho MS, Reis MG, Ko AI (2008) Impact of Environment and Social Gradient on Leptospira Infection in Urban Slums. PLoS Negl Trop Dis 2(4): e228. doi:10.1371/journal.pntd.0000228

[2]    Ko AI, Reis MG, Ribeiro Dourado CM, Johnson WD Jr, Riley LW and the Salvador Leptospirosis Study Group. (1999) Urban epidemic of severe leptospirosis in Brazil. Lancet 354: 820–825. doi:10.1016/S0140-6736%2899%2980012-9.

Advantages of Ontological Standards in Scholarly Publishing

Scholarly authoring and publishing is in the throes of a revolution, as the full potential of on-line publishing is explored. Semantic publishing is one aspect of this, namely
the use of web and semantic web technologies to enhance a published document such as a journal article so as to enrich its meaning, facilitate its automatic discovery, enable its linking to semantically related articles, provide access to data within the article in actionable form, and allow integration of data between papers [1].

As confirmed by a number of recent initiatives – including the Elsevier Grand Challenge and its Executable Paper Challenge, the Beyond The PDF Workshop, the Beyond Impact Workshop, the First International Workshop about Semantic Publication (SePublica 2011), the upcoming Schloss Dagstuhl Perspectives Workshop entitled The Future of Research Communication, and the Special Issue of the Semantic Web Journal on New Models of Semantic Publishing in Science, which is open for submissions until 15 September 2011 – semantic publishing and scholarly citation using web standards are presently two of the most interesting topics within the scientific publishing domain.

Yet, to date, publishers have not adopted web standards for their day-to-day work, but rather employ a variety of proprietary XML-based informational models and document type definitions (DTDs). While such independence was reasonable in the pre-web world of paper publishing, it now appears anachronistic, since publications and their metadata are incompatible, requiring hand-crafted mappings to convert from one to another. For a large community such as publishers, this lack of standard definitions that could be adopted and reused across the entire industry represents losses in terms of money, time and effort.

In contrast, modern web information management techniques employ standards such as RDF and OWL2 to encode information in ways that permit computers to query metadata and integrate web-based information from multiple resources in an automated manner. Since the processes of scholarly communication are central to the practice of science, it is essential that publishers now adopt such standards to permit inference over the entire corpus of scholarly communication represented in journals, books and conference proceedings.

The SPAR (Semantic Publishing and Referencing) Ontologies (http://purl.org/spar/), introduced in previous blog posts [2, 3], are specially tailored to the requirements of authors, publishers and their readers, and form key components of this semantic publishing revolution, as do the tools LODE [4] and Graffoo [5] that permit these (and other) ontologies to be documented and visualized in complementary ways. We commend their use to the scholarly publishing community.

[1] David Shotton, Katie Portwin, Graham Klyne, Alistair Miles David Shotton (2009) Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Computational Biology 5(4): e1000361. doi:10.1371/journal.pcbi.1000361.

[2] David Shotton (2010) Introducing the Semantic Publishing and Referencing (SPAR) Ontologies. JISC Open Citations Blog, 14 October 2010. http://opencitations.wordpress.com/2010/10/14/introducing-the-semantic-publishing-and-referencing-spar-ontologies/.

[3] David Shotton (2011) New web site for the SPAR ontologies. JISC Open Citations Blog, 25 February 2011. http://opencitations.wordpress.com/2011/02/25/new-web-site-for-the-spar-ontologies/.

[4] David Shotton (2011) Using LODE for ontology visualization. JISC Open Citations Blog, 25 February 2011. http://opencitations.wordpress.com/2011/02/25/using-lode-for-ontology-visualization/. 

[5] David Shotton (2011) Graffoo, a Graphical Framework for OWL Ontologies. JISC Open Citations Blog, 29 June 2011. http://opencitations.wordpress.com/2011/06/29/graffoo-a-graphical-framework-for-owl-ontologies/.