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.

 

Using FaBiO to describe data entities

In addition to using CiTO and CiTO4Data to describe relationships of relevance to data entities, as discussed in the previous blog post, FaBiO, the FRBR aligned Bibliographic Ontology described elsewhere, another member of the suite of SPAR (Semantic Publishing and Referencing) Ontologies, also has a number of classes and properties specifically designed for addressing data, software, metadata and other non-bibliographic entities. The purpose of this short post is simply to list these in one place.

Sub-classes of fabio:Work

fabio:ControlledVocabulary, sub-class of fabio:Vocabulary, with sub-classes

                    fabio:AuthorityFile

                    fabio:Ontology

                    fabio:Taxonomy

                    fabio:Thesaurus

fabio:Dataset

fabio:Image, with sub-classes

                    fabio:MovingImage

                    fabio:StillImage

fabio:Metadata, with sub-classes

                    fabio:ApplicationProfile

                    fabio:BibliographicMetadata

                    fabio:CitationMetadata

                    fabio:EntityMetadata

                    fabio:ProjectMetadata

fabio:Model

fabio:Specification, with sub-classes

                    fabio:Algorithm

                    fabio:VocabularyMapping

                    fabio:Workflow among others

fabio:SoundRecording

Sub-classes of fabio:Expression

fabio:ComputerProgram

fabio:DataFile

fabio:DataBase, with sub-classes

                    fabio:RelationsDataBase

                    fabio:Triplestore among others

fabio:DataRepository

fabio:Figure

fabio:MetadataDocument

fabio:Movie, with sub-class

                    fabio:Film

fabio:Repository, with sub-classes

                    fabio:DataRepository

                    fabio:DocumentRepository

                    fabio:WebArchive

fabio:Spreadsheet

fabio:SupplementaryInformationFile

fabio:Table

fabio:VocabularyDocument, with sub-class

                    fabio:OntologyDocument

Sub-classes of fabio:Manifestation

fabio:DigitalManifestation

Sub-classes of fabio:Item

fabio:DigitalItem, with sub-class

                    fabio:ComputerFile

Object properties

fabio:stores, and its inverse         fabio:isStoredOn

Data properties

fabio:hasDepositDate

fabio:hasEmbargoDate

prism:versionIdentifier

/end

BIBO2SPAR, an RDF Mapping of BIBO to the SPAR Ontologies

In the previous blog post, I made a textual comparison between BIBO v1.3, the Bibliographic Ontology developed by Bruce D’Arcus and Frédérick Giasson, and FaBiO, the FRBR-aligned Bibliographic Ontology.

In this post, I wish to introduce our RDF mapping of BIBO (version 1.3, undated, downloaded from http://purl.org/ontology/bibo/) to the SPAR (Semantic Publishing and Referencing) Ontologies, particularly to FaBiO (version 1.1, dated 23-06-2011, downloadable from http://purl.org/spar/fabio/), to permit cross-walk between these two systems.

The mapping takes the form of an alphabetical listing of all BIBO classes, object properties and data properties, for each of which is provided a SKOS mapping to equivalent classes, object properties or data properties in FaBiO or one of the other SPAR ontologies, or to relevant terms in FRBR, PRISM, FOAF, SKOS or Dublin Core Metadata Initiative Terms, where such a mapping is possible. Where it is not, a note is included to explain why.

Note that most of the classes in FaBiO are arranged according to the FRBR data model into fabio:Works (69 sub-classes), fabio:Expressions (92 sub-classes), fabio:Manifestations (10 sub-classes) and fabio:Items (4 sub-classes). 38 of the BIBO classes are sub-classes of bibo:Document, which roughly corresponds to fabio:Expression.

Note also that, because of the ambiguity and multiplicity of meanings of the word “document”, FaBiO intentionally lacks the class fabio:Document, using instead the generic term fabio:Expression and more specific sub-classes. In contrast, BIBO classifies things as diverse as films, slideshows and web pages as sub-classes of bibo:Document.

Note further that BIBO contains classes that describe social events, such as bibo:Interview and bibo:Performance, and that describe specific legal documents such as bibo:LegalDecision and bibo:Legislation. These have no equivalents in the SPAR Ontologies.

The mapping document, BIBO2SPAR, is written as validated RDF in Turtle format, and is available at https://sempublishing.svn.sourceforge.net/svnroot/sempublishing/SPAR/BIBO2SPAR.ttl

In the mappings, the BIBO class or property name is given on the left of each line, followed by the SKOS mapping relationship and the equivalent class or property name used in the SPAR ontologies, e.g.

bibo:AudioDocument skos:exactMatch fabio:AudioDocument .

This mapping document has been prepared by and is copyright © David Shotton, University of Oxford, and Silvio Peroni, University of Bologna, 23 June 2011, and is published as open data under a Creative Commons 2.5 attribution license.

Please contact <david.shotton@zoo.ox.ac.uk> or <speroni@cs.unibo.it> for further information.

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/.

Categorising bibliographic resources with FaBiO and SKOS

One of the most important need for a publisher is to categorising each bibliographic entity it produces by adding free-text keywords and/or specific terms structured according to recognised classification systems and/or thesauri specific for certain academic disciplines. Academics have the same need when annotating bibliographic references.

SKOS, the Simple Knowledge Organization System [1], is an RDFS model to support the use of knowledge organization systems (KOS) such as thesauri, classification schemes, subject heading lists and taxonomies within the framework of the Semantic Web. The reception of this language has been particularly positive: a large number of well-known thesauri and classification systems, including the Medical Subject Headings (MeSH) and the Library of Congress Subject Headings (LCSH), have started to convert their respective specifications into SKOS documents. This makes SKOS the de facto standard for encoding controlled vocabularies for the Semantic Web, and it is in this role that we have employed it within FaBiO.

While, through FaBiO, the FRBR-aligned Bibliographic Ontology, the definition of keywords is possible using the PRISM property prism:keyword, terms from thesauri, structured vocabularies and classification systems are best described using SKOS. To facilitate this, FaBiO extends some classes and properties of SKOS as shown in the following Graffoo diagram.

The extensions to the common SKOS classes and relations implemented in FaBiO

As shown, any FRBR endeavour can be associated with one or more descriptive terms (fabio:hasSubjectTerm fabio:SubjectTerm, a sub-class of skos:Concept) found in a specific dictionary (fabio:TermDictionary, a sub-class of skos:ConceptScheme) that is relevant to one or more particular disciplines (fabio:hasDiscipline fabio:SubjectDiscipline, also a sub-class of skos:Concept) describing a field of knowledge or human activity such as Computer Science, Biology, Economics, Cookery or Swimming. These discipline names (fabio:SubjectDiscipline) are recorded within a discipline dictionary (fabio:DisciplineDictionary, also a sub-class of skos:ConceptScheme).

For example, “cell”, “mitochondrion” and “Cell Biology” are members (fabio:SubjectTerms) of the Cell Biology Term Dictionary, a particular fabio:TermDictionary. This Cell Biology Term Dictionary has a scientific subject discipline (fabio:hasSubjectDiscipline), revealed by its name, of “Cell Biology”. This subject discipline is a member of the class fabio:SubjectDiscipline, and is contained within a fabio:DisciplineDictionary entitled “Science Subject Dictionary”.

Of course, the granularity of application of such an information model is up to the user, since from the point of view of the cell biology specialist, “cell biology” is his subject discipline, whereas from the point of view of a librarian cataloguing books, “cell biology” might be a subject term.

The following RDF example (in Turtle) shows how these concepts can be used to enrich a bibliographic record:

@prefix skos: <http://www.w3.oeg/2004/02/skos/core#>
@prefix acm: <http://www.acm.org/class/1998/> .
@prefix dbpedia: <http://dbpedia.org/resource/> .
@prefix wiley: <http://onlinelibrary.wiley.com/doi/> .

:intertextual-semantics a fabio:ResearchPaper
; dcterms:title “Intertextual semantics: A semantics for information design”
; fabio:hasPortrayal wiley:10.1002/asi.21134/full
; prism:keywords “semantics of markup” , “semiotic application” , “xml”
; fabio:hasSubjectTerm acm:markup-languages , acm:semantics .

acm:markup-languages a fabio:SubjectTerm
; skos:prefLabel “Markup languages”
; skos:inScheme <http://www.acm.org/class/1998>
; skos:broader acm:document-preparation .


acm:semantics a fabio:SubjectTerm
; skos:prefLabel “Semantics”
; skos:inScheme <http://www.acm.org/class/1998>
; skos:broader acm:formal-definitions-and-theory .


<http://www.acm.org/class/1998> a fabio:TermDictionary
; skos:prefLabel “The 1998 ACM Computing Classification System”
; fabio:hasDiscipline dbpedia:Computer_science .

[1] 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/.

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.

Introducing the Semantic Publishing and Referencing (SPAR) Ontologies

This blog post is to introduce the first four ontologies of SPAR, the Semantic Publishing and Referencing Ontologies, an integrated ecosystem of generic ontologies shown diagrammatically in the ‘flower’ diagram below (Figure 1). The ontologies can be used either individually or in conjunction, as need dictates. Each is encoded in the Web ontology language OWL 2.0. Together, they provide the ability to describe far more than simply bibliographic entities such as books and journal articles, by enabling RDF metadata to be created to relate these entities to reference citations, to bibliographic records, to the component parts of documents, and to various aspects of the scholarly publication process.

Flower diagram of the SPAR ontologies

Figure 1: The flower diagram, created by Benjamin 0’Steen, showing the component ontologies of SPAR.

The first four ontologies, FaBiO, CiTO, BiRO and C4O, which are now available for inspection, comment and use, are useful for describing bibliographic objects, bibliographic records and references, citations, citation counts, citation contexts and their relationships to relevant sections of cited papers, and the organization of bibliographic records and references into bibliographies, ordered reference lists and library catalogues.

Four additional ontologies, DoCO, PRO, PSO and PWO, are in preparation to provide structured controlled vocabularies for document components, publishing roles, publishing status and publishing workflows. A simple architectural diagram of the eight SPAR ontologies is shown in Figure 2.

SPAR architecture diagram

Figure  2: A simple architectural diagram, created by Silvio Peroni, showing the interactions and dependencies between the component ontologies of SPAR. Four ontologies (DoCO, PRO, PSO and PWO), some of which will import FOAF (http://xmlns.com/foaf/spec/20100809.rdf), are shown with faint outline because they are still under development.

The original motivation for creating the first of these ontologies, the Citation Typing Ontology CiTO, was provided by the semantic publishing work undertaken in 2008, described in [3]. Version 1.6 of the original CiTO ontology developed from that work is described in [4].

Since that publication, as part of a harmonization activity with the SWAN ontologies (http://swan.mindinformatics.org/ontology.html) described in [5], we have separated out from CiTO those aspects describing bibliographic entities into FaBiO, the FRBR-aligned Bibliographic Ontology, and those aspects describing the quantification of citations into C4O, the Citation Counting and Context Characterization Ontology, leaving the current version of CiTO (v2.0) with the sole role of describing the nature and character of the citations themselves.

Where appropriate, the SPAR ontologies, specifically FaBiO and BiRO, the Bibliographic Reference Ontology, employ the FRBR (Functional Requirements for Bibliographic Records) classification model, a conceptual entity-relationship model developed by the International Federation of Library Associations and Institutions (IFLAI) as a “generalized view of the bibliographic universe, intended to be independent of any cataloging code or implementation” [1, 2].  FRBR distinguishes Works, Expressions, Manifestations and Items.

In FRBR, a Work is a distinct intellectual or artistic creation, an abstract concept recognized through its various expressions (for example, 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 example, as a journal article); a Manifestation of an expression of a work defines its particular physical or electronic embodiment (for example online, print or PDF); and an Item is a particular copy of that you might own (for example the print copy of a journal issue on your desk). FRBR is widely recognized as a sound fundamental model for bibliographic records, and permits a clarity of description that is lacking when using ‘flat’ ontologies and vocabularies that do not employ the FRBR data model.

While the individual ontologies will be described in greater detail in subsequent blog posts and papers, their characteristics and benefits can be summarized as follows:

SPAR, the Semantic Publishing and Referencing Ontologies

  • An integrated ecosystem of independent and reusable ontology modules, capable of use to create comprehensive machine-readable RDF metadata for semantic publishing and referencing, comprising FaBiO, CiTO, BiRO, C4O, DoCO, PRO, PSO and PWO.

FaBiO, the FRBR-aligned Bibliographic Ontology (version 1.0; http://purl.org/spar/fabio/)

  • An ontology, structured according to the FRBR data model, to permit the description of bibliographic entities.
  • Comprehensive coverage of publication entity types, including born-digital entities.
  • Imports the FRBR Core ontology.
  • Uses PRISM terminology.
  • Extends the FRBR data model by the provision of new properties linking Works and Manifestations (fabio:hasManifestation and fabio:isManifestationOf), Works and Items (fabio:hasProtrayal and fabio:isPortrayedBy), and Expressions and Items (fabio:hasRepresentation and fabio:isRepresentedBy).
  • Harmonized with the SWAN ontologies (http://swan.mindinformatics.org/ontology.html), with the SWAN Citations Module deprecated in favour of using FaBiO to describe bibliographic entities.
  • RDF mappings of BIBO classes and properties to FaBiO in preparation.
  • RDF mappings of BibTEX entities to FaBiO to follow.

CiTO, the Citation Typing Ontology (version 2.0; http://purl.org/spar/cito/)

  • An ontology to permit the characterization of the type or nature of citations, both factual (e.g. cito:citesAsMetadataDocument; cito:sharesAuthorsWith) and rhetorical (e.g. cito:confirms, cito:qualifies), able to deal with both direct and explicit, and indirect and implicit citations.
  • Integrated with the SWAN Scientific Discourse Relationships Module (http://swan.mindinformatics.org/spec/1.2/scientificdiscourse.html).

BiRO, the Bibliographic Reference Ontology (version 1.0; http://purl.org/spar/biro/)

  • An ontology, structured according to the FRBR data model, to define bibliographic records (as subclasses of frbr:Work) and bibliographic references (as subclasses of frbr:Expression), and their compilation into bibliographic collections and bibliographic lists, respectively.
  • Imports the FRBR Core Ontology (http://purl.org/vocab/frbr/core).
  • Imports the SWAN Collections Ontology (http://swan.mindinformatics.org/ontologies/1.2/collections.owl) to permit the description of ordered lists.
  • Provides a logical system for relating an individual bibliographic reference, such as appears in the reference list of a published article (which may lack the title of the cited article, the full names of the listed authors, or indeed the full list of authors):
  1. to the full bibliographic record for that cited article, which in addition to missing reference fields may also include the name of the publisher, and the ISSN or ISBN of the publication;
  2. to collections of bibliographic records; and
  3. to bibliographic lists, such as reference lists and library catalogues.
  • Has the ability, used in conjunction with the SWAN Collections Ontology, to specify ordered lists:
  1. of authors,
  2. of references,
  3. of all the in-text reference pointers within an article, and
  4. of those in-text reference pointers specific for a single reference.

C4O, the Citation Counting and Context Characterization Ontology (version 1.0; http://purl.org/spar/c4o/)

  • An ontology that permits the characterization of bibliographic citations in terms of their number and their context.
  • Imports BiRO, and thus indirectly imports the FRBR Core Ontology and the SWAN Collections Ontology.
  • Provides the ontological structures to permit the number of citations a cited entity has received globally to be recorded, as determined by a bibliographic information resource such as Google Scholar, Scopus or Web of Knowledge on a particular date.
  • Provides the ontological structures to permit recording of the number of in-text citations of a cited source, (i.e. number of in-text reference pointers to a single reference in the citing article’s reference list).
  • Enables ontological descriptions of the context within the citing document in which an in-text reference pointer appears.
  • Permits that context to be related to relevant textual passages in the cited document.

N.B. The following four ontologies are under development, and will be published shortly.

DoCO, the Document Components Ontology

  • An ontology for the characterization of the component parts of a bibliographic document.
  • Provides a structured vocabulary of document components (e.g. Introduction, Discussion, Acknowledgements, Reference List, Figures, Appendix) in OWL, enabling these to be described in RDF.

PRO, the Publication Roles Ontology

  • An ontology for the characterization of the roles of agents (people, corporate bodies and computational agents; e.g. author, editor, reviewer, publisher, librarian) in the publication process, as they relate to bibliographic entities
  • Permits the recording of time/date information about when roles are held.

PSO, the Publications Status Ontology

  • An ontology for the characterization of the status of a document and other bibliographic entities at various stages in the publication process (e.g. submitted manuscript, rejected manuscript, accepted manuscript, proof, Version of Record, catalogued book).

PWO, the Publications Workflow Ontology

  • An ontology for the characterization of the main stages in the workflow associated with the publication of a document (e.g. under review, XML capture, page design, publication to Web).

Further blog posts will describe each of the SPAR ontologies in greater detail, will give examples of their use in encoding bibliographic and referencing information, and will describe mapping of other bibliographic metadata systems that do not employ the FRBR data model to FaBiO, specifically of BIBO, the non-FRBR bibliographic ontology, and of BiBTEX terminologies.

We invite community feedback and engagement on the four published SPAR ontologies, their improvement and their application.

This work forms part of the JISC Open Citations Project described in this blog.

The relevant hash tags when referring to this post are #jiscopencite and #spar.

David Shotton and Silvio Peroni
University of Oxford, October 2010

References

[1] Saur KG: FRBR (Functional Requirements for Bibliographic Records) Final Report. International Federation of Library Associations and Institutions; 1998. http://www.ifla.org/files/cataloguing/frbr/frbr_2008.pdf.
[2] Tillett B: What is FRBR? A Conceptual Model for the Bibliographic Universe. Washington DC, USA: Library of Congress, Cataloguing Distribution Service; 2003. http://www.loc.gov/cds/downloads/FRBR.PDF.
[3] Shotton D, Portwin K, Klyne G, Miles A: Adventures in semantic publishing: exemplar semantic enhancements of a research article. PLoS Comput Biol 2009, 5:e1000361. http://dx.doi.org/10.1371/journal.pcbi.1000361.
[4] Shotton D: CiTO, the Citation Typing Ontology. Journal of Biomedical Semantics 2010, 1 (Suppl. 1): S6. http://dx.doi.org/10.1186/2041-1480-1-S1-S6.
[5] Ciccarese P, Shotton D, Peroni S and Clark T: CiTO + SWAN: The web semantics of bibliographic records, citations, evidence and discourse relationships. (Submitted for publication).

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