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Outline

Outline. In this brief presentations, I will mention Our initial work on semantic enhancement that led to CiTO The SPAR Semantic Publishing and Referencing Ontologies examples of usage Citations in Context The Open Citations Project The Dryad data repository.

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Outline

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  1. Outline • In this brief presentations, I will mention • Our initial work on semantic enhancement that led to CiTO • The SPAR Semantic Publishing and Referencing Ontologies • examples of usage • Citations in Context • The Open Citations Project • The Dryad data repository

  2. http://dx.doi.org/10.1371/journal.pntd.0000228.x001

  3. An annotated reference list • The act of citation of others' preceding work is a central social process in the practice of science, formalized in the reference lists at the end of articles. • The first three references from the reference list of our enhance version of Reis et al. (2008) are shown, with the citation typing display turned on • This work led to the initial version of CiTO, the Citation Typing Ontology

  4. CiTO • CiTO permits the existence of a citation between a citing work and a cited work to be recorded in RDF <http://example1.com/citingwork> cito:cites <http://example2.com/citedwork> . • CiTO permits the nature of the citation between a citing work and a cited work to be characterized, • both factually: reviews, sharesAuthorsWith, usesMethodIn, etc • and rhetorically: confirms, corrects, refutes, etc • CITO permits the construction and interrogation of citation networks

  5. Conversion of hypothesis to ‘fact’ by citation alone Citation: Steven Greenberg (2009). How citation distortions create unfounded authority: analysis of a citation network. British Medical Journal 339: b2608.

  6. SPAR – Semantic Publishing and Referening Ontologies

  7. The SPAR Ontologies • FaBiO http://purl.org/spar/fabio/ • CiTO http://purl.org/spar/cito/ • C40 http://purl.org/spar/c4o/ • BiRO http://purl.org/spar/biro/ • DoCO http://purl.org/spar/doco/ • PRO http://purl.org/spar/pro/ • PSO http://purl.org/spar/pso/ • PWO http://purl.org/spar/pwo/ Viewed using LODE, the Live OWL Documentation Environment http://lode.sourceforge.net/

  8. Viewing the SPAR Ontologies • We use content negotiation to deliver • the OWL2 ontology itself when one of these SPAR Ontology purls is accessed using an ontology editing application such as Protégé or the NeOn Toolkit • or a human-readable description of the ontology when one of these SPAR Ontology purls is accessed using a Web browser • For the latter, we use LODE, the open source Live OWL Documentation Environment developed by Silvio Peroni – http://lode.sourceforge.net/ • LODE automatically extracts all the ontology components from an OWL ontology, and renders them as ordered lists, together with their textual definitions, in a human-readable HTML page designed for browsing and navigation by means of embedded links • The CSS used to generate the LODE HTML page is based on the CSS for W3C Recommendation documents

  9. SPAR and SWAN • SPAR import and use the SWAN Collections Ontology for the creation of ordered lists, and SWAN’s FOAF Essentials for describing individuals • Reciprocally, FaBiO replaces the deprecated SWAN Citations Module, and the SWAN Discourse Relationships Ontology has been revised to work with CiTO • Both SPAR and SWAN import FRBR-DL, an OWL-DL version of FRBR Core, created jointly by Silvio Peroni and the SWAN developer Paolo Cicarrese • A paper describing this harmonization activity is forthcoming in the Journal of Biomedical Informatics

  10. Uses of C4O and FaBiO • C4O, the Citation Counting and Context Characterization Ontology, permits citation frequencies to be recorded • both local: e.g. “Paper A cites Paper B once, but cites Paper C ten times” • and global: e.g. “Paper C is cited 234 times according to Scopus” • FaBiO, the FRBR-aligned Bibliographic ontology, permits characterization of the cited works themselves as journal articles, books, etc. • FaBiO uses the FRBR entity model to make distinctions between • Work An abstract concept, e.g. your latest research paper • Expression A realization of that work, e.g. the submitted preprint • Manifestation An embodiment of that manifestation, e.g. as a PDF • Examples of annotations using FaBiO • Sub-classes of Work include DiscussionResearchPaper • Sub-classes of Expressioninclude BlogPostJournalArticle • Sub-classes of Manifestationinclude Blog PrintObject

  11. Ko et al. 1999 c4o:GlobalCitationCount 206 SPAR metadata: cito:usesDataFrom fabio:ReferenceWork, fabio:Book pso:notPeerReviewed c4o:GlobalCitationCount 19 Citation display from Reis et al. using SPAR RDF metadata • Here, using a plugin we developed for the RDF visualization program Exhibit, references are displayed on a temporal axis, colour-coded to indicate journal articles, reviews and books, and with diameters and y-axis position determined by their global citation frequency as determined from Google Scholar

  12. Citation context • C4O can also be used to relate the context of a citation to relevant passages in the cited paper • This enables the development of “Citation in Context” services • as exemplified in our semantically enhanced Reis et al PLoS paper • as demonstrated by Stephen Wan in his CSIBS system, finalist in the 2009 Elsevier Grand Challenge

  13. A demonstration of Citations in Context • Open our enhanced version of the Reis et al. (2008) PLoS Neglected Tropical Diseases paper at http://dx.doi.org/10.1371/journal.pntd.0000228.x001 • Go to the Introduction section of the paper by clicking the “Introduction” navigation link at the top of the document • Hover your mouse over the second in-text reference pointer to Reference 6 • “Urban epidemics of leptospirosis now occur in cities throughout the developing world during seasonal heavy rainfall and flooding [6],[11]–[18].” • A browser popup will display a relevant sentence and a thumbnail image relating to Figure 2 in the cited paper by Ko et al. (1999) Lancet 354: 820-825

  14. Encoding Citations in Context using SPAR • A diagram demonstrating the way that all the relationships involved in Citations in Context can be encoded using CiTO, C4O, BiRO, FRBR-DL and Dublin Core RDF metadata is shown on the next slide

  15. The use of DoCO to describe document front matter

  16. Use of DoCO to describe body text

  17. Use of DoCO to describe body text and references

  18. The use of DoCO to describe Methods and Materials

  19. Use of DoCO to describe a figure and its legend

  20. Use of DoCO to describe a figure and its legend

  21. The Open Citations Project Partners • PLoS and Biomed Central (Open Access publishers) • British Library (for UK Pubmed Central and DataCite DOIs) • European Bioinformatics Institute (for UKPMC and CiteXplore) • University of Cambridge: Open Bibliography sister project • Open Knowledge Foundation’s Bibliographic Working Group • Bibliographic Knowledge Network: Will facilitate interoperability with related projects in the USA • Talis, who will host the triples, and CrossRef • We welcome involvement of others • To establish OpenCitations.net, a public RDF triplestore of Linked Open Data describing biomedical literature citations • To harvest reference lists from open access articles in UK Pubmed Central • To publish reference lists from individual papers in RDF using SPAR ontologies

  22. An example of citation metadata in RDF <http://dx.doi.org/10.1371/journal.pntd.0000228> cito:cites<http://dx.doi.org/10.1016/S0140-6736(99)80012-9># Reference [6]; frbr:part [a biro:BibliographicReference; c4o:hasInTextCitationFrequency "10"^^xsd:nonNegativeInteger; biro:references <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> ] ; cito:obtainsBackgroundFrom <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> ; cito:usesDataFrom <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> ; cito:confirms <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> ; cito:extends<http://dx.doi.org/10.1016/S0140-6736(99)80012-9> ; cito:sharesAuthorsWith <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> . # Reference [6] <http://dx.doi.org/10.1016/S0140-6736(99)80012-9> dcterms:bibliographicCitation "Ko AI, Reis MG, Ribeiro Dourado CM, Johnson WD Jr, Riley LW (1999). Urban epidemic of severe leptospirosis in Brazil. Salvador Leptospirosis Study Group. Lancet 354: 820-825."; prism:publicationDate "1999-09-04"^^xsd:date ; cito:isCitedBy <http://dx.doi.org/10.1371/journal.pntd.0000228> ; frbr:realizationOf [ a fabio:ResearchPaper ] ; # work a fabio:JournalArticle ; # expression pso:holds [a pso:StatusInTime ; pso:withStatus pso:peer-reviewed ] ; # Google Scholar on 11 March 2009: Cited 206 times. c4o:hasGlobalCitationFrequency [ a c4o:GlobalCitationCount ; c4o:hasGlobalCountValue "206"^^xsd:integer ; c4o:hasGlobalCountSource <http://scholar.google.com> ; c4o:hasGlobalCountDate "2009-03-11"^^xsd:date ] .

  23. PubmedCentral started receiving papers in 2000. ~10% of its holdings were published in earlier years 110,567 open access papers in PubmedCentral, citing a total of 1,694,905 unique papers

  24. 2,353 open access papers on HIV/AIDS in PMC, citing a total of 28,067 unique papers Despite the citing papers being a sub-set, all the key papers in the field are cited

  25. The DRYAD Project http://datadryad.org/repo • Dryad is a new repository of data underlying scientific publications, with an initial focus on the fields of evolution and ecology • Datasets are published with unique identifiers (DOIs) under Creative Commons ‘CC-Zero’ public domain data publication licenses • Better alternative than publishing as Supplementary Data Files • Open, DOIs, proper curation • Data to be made available to peer reviewers • We are working , in collaboration with the British Library, the Digital Curation Centre and the US Dryad team at NESCent in North Carolina • to internationalize Dryad, with a mirror site at the BL, and • to expanding its journal range into epidemiology and infectious disease • Dryad has a need for reciprocal citation between datasets and papers, and we are working to move its metadata from XML to RDF using the SPAR ontologies

  26. The SPAR Community • SPAR provides a suite of ontologies suitable for datasets as well as papers • SPAR permits types of description not covered in the preceding examples, e.g. PRO and PSO permit description of publishing roles (e.g. reviewer) and status (e.g. peer-reviewed) • PWO, a simple Publishing Workflows Ontology, can be used to encode the steps in Phil’s publishing workflow • Our desire now is to see SPAR applied • CiTO is already being used in CiteULike • Utopia adoption of SPAR adoption • The European Patent Office and several publishers very interested • I am now seeking to form a collaborative community of developers and users to provide long-term support for SPAR

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