Comments on the paper Ceci n’est pas un hamburger

Very VERY occasionally I read a paper that is so well written, and which addressed the points so accurately and so eloquently, that I rejoice.  The paper by Pettifer et al. entitled Ceci n’est pas un hamburger: modelling and representing the scholarly article that appeared in Learned Publishing last October [1], is one of this special handful. 

It is beautifully written, and the scope of its coverage is highly pertinent to the recent discussions on the future of research communication detailed in the previous post.  It also has the benefit of being published as an Open Access paper in what is otherwise a subscription access journal. 

I particularly liked the authors’ evaluation of FRBR‘s classification into works, expressions and manifestations to describe the relative benefits and drawbacks of PDF, XML, and RDF as representations of a journal article, since that is exactly what Silvio Peroni and I modelled in FaBiO, the FRBR-aligned Bibliographic Ontology.

The paper is also an excellent introduction to Utopia Documents, the ‘smart’ PDF reader that the authors have developed, which is used to create the Semantic Biochemical Journal, and which is to be highly recommended for personal use to enrich the experience of reading articles in PDF format on-line.  The Utopia Documents software is freely available, and can be downloaded from http://www.utopiadocs.com.

[1] Pettifer S, McDermott P, Marsh J, Thorne D, Villeger A and Attwood TK (2011).  Ceci n’est pas un hamburger: modelling and representing the scholarly article.  Learned Publishing, 24 (3): 207-220.  http://dx.doi.org/10.1087/20110309.

Cite this article as: davidshotton, "Comments on the paper Ceci n’est pas un hamburger," in OpenCitations blog, 10/01/2012, https://opencitations.hypotheses.org/304.

 

Comparison of BIBO and FaBiO

BIBO v1.3, the Bibliographic Ontology developed by Bruce D’Arcus and Frédérick Giasson [1], was the first OWL ontology dedicated to describing bibliographic entities, and has attracted a wide group of users. It provided the much-needed ability to describe the nature of cited works in RDF to a high degree of granularity, in terms of Title, Abstract, Journal, Volume, Pages, ISSN, DOI, dataCopyrighted, editor, etc.

FaBiO, the FRBR-aligned Bibliographic Ontology, which was created more recently and was introduced in a previous blog post [2], bears many similarities with BIBO, including its overall scope and intention, and the inclusion of PRISM and DC Terms data properties. A clear comparison of these two ontologies, and the provision of a mapping between them, is long overdue.

The primary differences between FaBiO and BIBO are as follows:

  1. While BIBO is a ‘flat’ ontology, FaBiO is structured according to the FRBR conceptual model, in which publication entities are described from four different and correlated points of view, those of Work, Expression, Manifestation and Item, each of which is a FRBR Endeavour, as defined in a previous blog post. This structure has been introduced to provide greater expressivity. For example, using FaBiO one can describe a fabio:ResearchPaper that can be published as a fabio:JournalArticle, or alternatively as a fabio:ConferencePaper or a fabio:BookChapter. BIBO has the class bibo:AcademicArticle, which conflated the two concepts ResearchPaper (a conceptual Work) and JournalArticle (an Expression of that Work).
  2. Great care has been taken to make the textual definitions of FaBiO classes accurate and expressive. Thus, while BIBO’s definition of bibo:Standard is “A document describing a standard”, FaBiO describes fabio:TechnicalStandard, which is a subclass of fabio:Specification, as “An official or public specification of, or requirement for, a technical method, practice, process or protocol that is involved in, for example, manufacturing, computation, electronic communication, or digital media.”
  3. FaBiO is larger than BIBO (211 rather than 69 classes, 69 rather than 52 object properties, 45 rather than 54 data properties, and 16 rather than 15 individuals), permitting greater expressivity.
  4. BIBO has a slight subject specialism in the area of legal documents (including bibo:Bill, bibo:Brief, bibo:CourtReporter, bibo:LegalCaseDocument, bibo:Statue). In addition to covering conventional scholarly works, BIBO also covers a few things outside the immediate realm of bibliographic entities, including social events (e.g. bibo:Hearing, bibo:Interview, bibo:Performance) and personal roles (e.g. bibo:interviewer, bibo:performer, bibo:producer). In contrast, FaBiO was developed to describe anything a research scientist might need to reference. Thus it lacks legal classes but includes classes that betray a preoccupation with academia and publications (e.g. fabio:ExaminationPaper, fabio:Preprint, fabio:SupplementaryInformationFile), funding and IPR (e.g. fabio:GrantApplication, fabio:PatentApplication), biomedical research (e.g. fabio:ClinicalTrialDesign, fabio:SystematicReview), research data (e.g. fabio:Dataset, fabio:Metadata, fabio:DataBase, fabio:DataRepository), computing (e.g. fabio:Algorithm, fabio:ComputerProgram), web communication (e.g. fabio:BlogPost, fabio:WikiEntry) and ontologies (e.g. fabio:ControlledVocabulary, fabio:Ontology, fabio:Thesaurus, fabio:Taxonomy), none of which are present in BIBO.
  5. FaBiO is not a stand-alone ontology, but is one of the SPAR (Semantic Publishing and Referencing) Ontologies, a suite of complementary and orthogonal ontologies outlined in two previous blog posts [2, 3], that cover all aspects of publishing, referencing and bibliographic endeavour.
  6. FaBiO and the other SPAR ontologies are written in OWL 2 DL, enabling them to be used in the Semantic Web with appropriate reasoners. In contrast, BIBO is in OWL Full, since it includes the RDF resources rdf:List, rdf:Seq and rdfs:Resource and the property rdf:value that cannot be included in proper OWL2 DL ontologies.
  7. BIBO contains a few elements that are not present within FaBiO, but that have equivalent elements within some of the other SPAR ontologies:
    1. the object properties bibo:cites and bibo:isCitedBy have equivalent properties in CiTO, the Citation Typing Ontology, where they have 32 sub-properties lacking in BIBO;
    2. classes to describe component parts of documents (e.g. bibo:DocumentPart) that are covered in DoCO, the Document Components Ontology;
    3. classes and properties to describe the status of documents (e.g. bibo:DocumentStatus, bibo:status), that are covered in PSO, the Publication Status Ontology.
  8. FaBiO and CiTO have been harmonized [4] with the SWAN (Semantic Web Applications in Neuromedicine) ontology ecosystem developed by Tim Clark and Paolo Ciccarese of Harvard University, which covers the domain of scientific discourse in general, with particular application to neuromedicine, and which is used particularly useful for characterizing rhetorical structures between documents. Since SWAN had been previously harmonized with the SIOC (Semantically-Interlinked Online Communities) ontology for describing blogs, wikis and discussion groups, this provides the basis of a powerful new web framework for scientific communications.
  9. For categorising bibliographic resources, FaBiO has been integrated with and extends SKOS, the Simple Knowledge Organization System [5] that supports the use of thesauri, classification schemes, subject heading lists, taxonomies and other knowledge organization systems within the framework of the Semantic Web, as described in a previous blog post.

The choice of whether to use BIBO or FaBiO depends upon whether BIBO possesses sufficient expressiveness for the task in hand, whether the user is prepared to put in the small degree of extra effort required to engage with the layered FRBR structure of FaBiO rather than the flat structure of BIBO, whether one requires the semantic reasoning support of an OWL 2 DL ontology, and whether the user requires integration with other ontologies such as CiTO and SWAN, that FaBiO provides.

To assist existing users of BIBO and the SPAR Ontologies to map between these two systems, we have used SKOS to prepare an RDF mapping document, BIBO2SPAR, that we describe in the following blog post.

[1] Bruce D’Arcus and Frédérick Giasson (2009). Bibliographic Ontology Specification. Specification Document, 4 November 2009. http://bibliontology.com/specification.

[2] David Shotton (2010) Introducing the Semantic Publishing and Referencing (SPAR) Ontologies. JISC Open Citations Blog, 14 October 2010. https://opencitations.hypotheses.org/16.

[3] David Shotton (2011) New web site for the SPAR ontologies. JISC Open Citations Blog, 25 February 2011. https://opencitations.hypotheses.org/55.

[4] Ciccarese P, Shotton D, Peroni S and Clark T (2011) CiTO + SWAN: The Web Semantics of Bibliographic Records, Citations, Evidence and Discourse Relationships. (Submitted for publication).

[5] Miles, A., Bechhofer, S. (2009). SKOS Simple Knowledge Organization System Reference. W3C Recommendation, 18 August 2009. World Wide Web Consortium. http://www.w3.org/TR/2009/REC-skos-reference-20090818/.

Cite this article as: davidshotton, "Comparison of BIBO and FaBiO," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/109.

Extending FRBR within FaBiO

FRBR, the Functional Requirements for Bibliographic Records [1] is a general model, proposed by the International Federation of Library Association (IFLA), for describing bibliographic documents. It works for both physical and digital resources and has proved to be very flexible and powerful. One of the most important aspect of FRBR is the fact that it is not associated with a particular metadata schema or implementation. Its defining characteristic is that FRBR describes all documents from four different and correlated points of view, those of Work, Expression, Manifestation and Item, each of which is a FRBR Endeavour.

A Work is a distinct intellectual or artistic creation, an abstract concept recognised through its various expressions. An example of a Work is your latest research paper.

An Expression is the specific form that a Work takes each time it is ‘realized’ in physical or electronic form. For your latest research paper, Draft 5, the preprint, and the published version to which the publisher assigned a unique DOI (Digital Object Identifier), are all Expressions of the same work.

A Manifestation of an expression of a scholarly work defines its particular physical or electronic embodiment. If your latest research paper appeared as an article in a print journal, in the on-line version of that journal as an HTML page, and also as a downloadable PDF file, these are three separate manifestations of the same ‘version of record’ Expression of your work, all bearing the same DOI.

In FRBR, an Item is one single exemplar copy of a Manifestation, i.e. a physical or electronic object that can be owned by a person, for example a particular HTML file on a web server, a printed copy of a journal article on your desk, or a PDF file of that article that you purchased from a publisher and that now resides in digital form on your computer hard drive.

There now exists two different implementations of the core concepts of FRBR using standards that permit the encoding of proper semantics: the first, authored in 2005 by Richard Newman and Ian Davis, is FRBR Core in RDFS, while the second, developed from the first in 2010 by Paolo Ciccarese and Silvio Peroni, is FRBR Core in OWL 2 DL.

FaBiO, the FRBR-aligned Bibliographic Ontology, previously described in this blog post, is an ontology for recording and publishing on the Semantic Web bibliographic records of scholarly endeavours that is structured according to the FRBR model of Works, Expressions, Manifestations and Items.

One of the explicit requests from publishers and end-users of FaBiO was to create shortcuts between particular combinations of FRBR endeavours C:\Documents and Settings\David Shotton\My Documents\Papers and books\Peroni paper CiTO and FaBiO\citofabio_01.odt\iml: – IFLAStudyGroupFRBR(between Work and Manifestation, between Work and Item, and between Expression and Item), since these were not part of the original FRBR model.

Let us introduce a bibliographic reference to illustrate this need:

Yves Marcoux, Élias Rizkallah (2009). Intertextual semantics: A semantics for information design. http://onlinelibrary.wiley.com/doi/10.1002/asi.21134/full.

In this reference, we have a FRBR work – the paper by Marcoux and Rizkallah – and the URL for a specific FRBR item that portrays that work, an HTML file containing the paper on the publisher’s web site. If we wished to link these concepts simply using the FRBR OWL ontology terms, we would be obliged to specify each intermediate FRBR endeavour, namely the expression and manifestation of that paper, even if we were not interested in doing that:

 @prefix wiley: <http://onlinelibrary.wiley.com/doi/> .

:intertextual-semantics a frbr:Work
; frbr:creator :marcoux , :rizkallah
; dcterms:title “Intertextual semantics: A semantics for information design”
; frbr:realization [ a frbr:Expression
; frbr:embodiment [ a frbr:Manifestation
; frbr:exemplar wiley:10.1002/asi.21134/full ] ] .

 In order to avoid this kind of verbosity, we have supplemented the existing FRBR object properties with three new FaBiO properties shown in the following figure: fabio:hasManifestation that links a Work directly to its Manifestations, fabio:hasPortrayal that links a Work directly to its Items), and fabio:hasRepresentation that links an Expression directly to its Items.


A Graffoo diagram showing the FRBR Core data model, supplemented with three new FaBiO properties.

Note: In Manchester Syntax, the “o” in each sub-property chain is the syntax mechanism for chaining properties.

These added properties allow us to treat the previous example in a less verbose way:

@prefix wiley: <http://onlinelibrary.wiley.com/doi/> .

:intertextual-semantics a frbr:Work
; frbr:creator :marcoux , :rizkallah
; dcterms:title “Intertextual semantics: A semantics for information design”
; fabio:hasPortrayal wiley:10.1002/asi.21134/full .

[1] IFLA Study Group on the Functional Requirements for Bibliographic Records (2009). Functional Requirements for Bibliographic Records Final Report. International Federation of Library Associations and Institutions. http://www.ifla.org/en/publications/functional-requirements-for-bibliographic-records.

Cite this article as: davidshotton, "Extending FRBR within FaBiO," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/95.
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