Semantic annotation of publication entities using the SPAR (Semantic Publishing and Referencing) Ontologies

Transcription

1 Beyond the PDF Workshop La Jolla 19 January 2011 Semantic annotation of publication entities using the SPAR (Semantic Publishing and Referencing) Ontologies David Shotton and Silvio Peroni Image Bioinformatics Research Group Department of Zoology University of Oxford, UK "It is a very sad thing that nowadays there is so little useless information Oscar Wilde

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3 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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5 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

6 CiTO CiTO permits the existence of a citation between a citing work and a cited work to be recorded in RDF < cito:cites < 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

7 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.

8 SPAR Semantic Publishing and Referening Ontologies

9 The SPAR Ontologies FaBiO CiTO C40 BiRO DoCO PRO PSO PWO Viewed using LODE, the Live OWL Documentation Environment

10 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 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

11 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

12 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 Discussion ResearchPaper Sub-classes of Expression include BlogPost JournalArticle Sub-classes of Manifestation include Blog PrintObject

13 Citation display from Reis et al. using SPAR RDF metadata SPAR metadata: cito:usesdatafrom fabio:referencework, fabio:book pso:notpeerreviewed c4o:globalcitationcount 19 Ko et al c4o:globalcitationcount 206 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

14 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

15 A demonstration of Citations in Context Open our enhanced version of the Reis et al. (2008) PLoS Neglected Tropical Diseases paper at 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:

16 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

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18 The use of DoCO to describe document front matter

19 Use of DoCO to describe body text

20 Use of DoCO to describe body text and references

21 The use of DoCO to describe Methods and Materials

22 Use of DoCO to describe a figure and its legend

23 Use of DoCO to describe a figure and its legend

24 The Open Citations Project 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 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

25 An example of citation metadata in RDF < cito:cites < # Reference [6]; frbr:part [a biro:bibliographicreference; c4o:hasintextcitationfrequency "10"^^xsd:nonNegativeInteger; biro:references < ] ; cito:obtainsbackgroundfrom < ; cito:usesdatafrom < ; cito:confirms < ; cito:extends < ; cito:sharesauthorswith < # Reference [6] < 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: "; prism:publicationdate " "^^xsd:date ; cito:iscitedby < ; 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 < ; c4o:hasglobalcountdate " "^^xsd:date ].

26 PubmedCentral started receiving papers in ~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

27 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

28 The DRYAD Project 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

29 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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