DataCite2RDF – Mapping DataCite Metadata Scheme Terms to ontologies

The DataCite Metadata Kernel version 2.0 [1] specifies the minimal metadata, and optional metadata, that should accompany a DataCite DOI for the identification of a published data entity. Within the Metadata Kernel document there is an XML mapping of these metadata terms, using DCMI Metadata Terms, and an example encoded in XML.

Silvio Peroni and I recently published a mapping of the DataCite metadata elements to RDF using ontology terms [2], in order to enable data repositories to publish DataCite metadata in RDF as Open Linked Data, enabling these metadata to be understood programmatically and integrated automatically with similar data from elsewhere.

Our mapping covers all the main terms, and the Relation Type sub-properties that describe the relationship of the related resource to the resource being registered, but does not address DataCite sub-terms, e.g. 2.2.1 nameIdentifierScheme.

Wherever possible, commonly used Dublin Core Elements, DCMI (Dublin Core Metadata Initiative) Metadata Terms, FOAF (Friend of a Friend Vocabulary) and PRISM (Publishing Requirements for Industry Standard Metadata) terms have been used.

These have been supplemented, as appropriate, by terms:

from FRBR (Functional Requirements for Bibliographic Records),

from the following SPAR (Semantic Publishing and Referencing) Ontologies:

                CiTO, Citation Typing Ontology

                FaBiO, FRBR-aligned Bibliographic Ontology, and

CiTO4Data, an extension of CiTO for datasets that provides the properties cito4data:compiles and cito4data:isCompiledBy that the DataCite Metadata Kernel requires;

and from a new DataCite Ontology (http://purl.org/spar/datacite/) that we created to provide the following four object properties lacking in other Ontologies:

                    datacite:hasPrimaryIdentifier

                    datacite:hasAlternateIdentifier

                    datacite:hasRelatedIdentifier

                    datacite:hasPersonalIdentifier

Use of DCMI Metadata Terms in RDF

An object property has a class or a URI as its object, while a data property has a literal (e.g. text, number, date) as its object, and may have a W3C XML Schema Definition Language (XSD) datatype qualifier, e.g. ^^xsd:date. (See http://www.w3.org/TR/xmlschema11-2/).

Many Dublin Core properties are not formally specified to be one or another, leading to potential confusion. In the following mapping, Dublin Core Elements are always used as data properties, while Dublin Core Metadata Initiative Metadata Terms are used either as data properties or as object properties, as helpfully specified by the Max Planck Digital Library in their document entitled How to use DCMI Metadata as linked data.  

In our DataCite2RDF mapping document [2], alternative mappings are given where appropriate, separated by semi-colons.  Both dc: and dcterms: properties are listed.  Preferred terms are shown bold.  RDF statements are given in Turtle notation.

Accompanying this DataCite2RDF mapping document, we published as Google docs both an RDF mapping of the DataCite XML example, and an RDF mapping of the metadata for a Dryad repository holding, showing how DataCite2RDF can be used for real data.

We welcome feedback on these documents: <david.shotton@zoo.ox.ac.uk> and <speroni@cs.unibo.it>.

[1]    The DataCite Metadata Kernel version 2.0 (2011). http://datacite.org/schema/DataCite-MetadataKernel_v2.0.pdf.

[2]     David Shotton and Silvio Peroni (2011). Mapping DataCite Metadata Scheme Terms (v2.0) to ontologies (DataCite2RDF). Google docs. https://docs.google.com/document/d/1paJgvmCMu3pbM4in6PjWAKO0gP-6ultii3DWQslygq4/edit?authkey=CMeV3tgF&hl=en_GB.

Cite this article as: davidshotton, "DataCite2RDF – Mapping DataCite Metadata Scheme Terms to ontologies," in OpenCitations blog, 30/06/2011, https://opencitations.hypotheses.org/139.

 

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

Cite this article as: davidshotton, "Using FaBiO to describe data entities," in OpenCitations blog, 30/06/2011, https://opencitations.hypotheses.org/131.

CiTO4Data – a new data-centric citation typing ontology

This is the first of a series of blog posts on the Open Citations blog that address the problem of citing data entities, for example a data package in a data repository, rather than bibliographic entities such as journal articles. For these purposes, the existence of DataCite to assign DOIs to datasets, and extensions to the SPAR (Semantic Publishing and Referencing) Ontologies to handle data items, are both important. This post addresses the second of these two issues.

As described in the previous blog post, CiTO, the Citation Typing Ontology, focuses on providing ontological properties to characterize citations of bibliographic entities. However, several of its relationships can also be used in relation to data entities:

Sub-classes of cito:cites

    cito:citesAsDataSource

    cito:citesAsEvidence

    cito:corrects

    cito:extends

    cito:updates

    cito:usesDataFrom

When attempting to map the DataCite metadata elements to ontology terms, to be described in a subsequent blog post, we encountered the DataCite requirement for the properties compiles and isCompiledBy, which are absent from CiTO and other ontologies that we know about and which cannot be conceived as relating to bibliographic entities.

Conscious of a growing need to specify metadata for data entities as well as bibliographic entities, and reluctant to include in CiTO relationships that cannot be applied to bibliographic entities, Silvio Peroni and I have thus created CiTO4Data, a new ontology within the SPAR ontology suite, to be found at http://purl.org/spar/cito4data/.

CiTO4Data, the Citation Typing Ontology for Data, is an extension ontology written in OWL 2 DL that imports CiTO, the Citation Typing Ontology, and adds extra object properties that are relevant only for datasets, computer programs and other similar digital objects, but not for conventional bibliographic entities.

To date, CiTO4Data adds just a single new object property

    cito4data:compiles

and its inverse

    cito4data:isCompiledBy

created to meet the need of encoding the DataCite Metadata Kernel v2.0 into RDF. We intend to expand CiTO4Data to include other properties relevant only for citing data entities, as the need arises.

NOTE: In the summer of 2012, we decided for simplicity to include these two properties within CiTO itself (as cito:compiles and cito:isCompiledBy), and to deprecate the CiTO4Data ontology.

Cite this article as: davidshotton, "CiTO4Data – a new data-centric citation typing ontology," in OpenCitations blog, 30/06/2011, https://opencitations.hypotheses.org/128.

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.

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/.

Cite this article as: davidshotton, "Categorising bibliographic resources with FaBiO and SKOS," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/101.

Functional clustering of CiTO properties

CiTO v2.0 contains just two main object properties, cito:cites and its inverse cito:isCitedBy, each of which as thirty-two sub-properties. Intentionally, these properties are not constrained as to domain or range, thereby maximising their applicability in a wide range of citation contexts. Additionally, CiTO contains one additional generic object property, cito:shareAuthorsWith, that may be used even outside a citation context.

Some have criticised CiTO for having too many properties, making it confusing for potential users, and Martin Fenner chose to use only the ten ‘most popular’ properties in his CiTO plug-in for WordPress, previously mentioned in this blog post. In response, I would point out that each property has a distinct and clearly defined meaning, and that together they provide an appropriate level of expressivity for effective use. Nevertheless, it is clearly difficult to conceptualize all the CiTO properties at one time, if they are being viewed using an ontology editor such as Protégé. I have thus created the following figure that groups CiTO properties by similarity, in the hope that this will facilitate choice of the most appropriate one.

Clustering of CiTO relationships by similarity

As shown in the figure, the CiTO properties and sub-properties (and, consequently, their inverses) may be classified as rhetorical (upper oval) and/or factual (lower oval, dark blue text), with the rhetorical properties being grouped in three sets depending on their connotation: positive (green), neutral or informative (blue) and negative (red). Five properties (in purple, within the overlap of the ovals) have both factual and rhetorical characteristics. The inverse properties are not shown.

Cite this article as: davidshotton, "Functional clustering of CiTO properties," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/91.

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/.

Cite this article as: davidshotton, "Advantages of Ontological Standards in Scholarly Publishing," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/87.

New web site for the SPAR ontologies

The last four SPAR ontologies – the Document Components Ontology DoCO, the Publishing Roles Ontology PRO, the Publishing Status  Ontology PSO and the Publishing Workflow Ontology PWO – were recently completed.  All eight SPAR ontologies have now been thoroughly revised and checked, and are stable and ready for use.   Descriptions of the ontologies are now provided at the new SPAR web site – http://purl.org/spar/ – which contains links to the ontologies themselves.

Cite this article as: davidshotton, "New web site for the SPAR ontologies," in OpenCitations blog, 25/02/2011, https://opencitations.hypotheses.org/55.

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).

Cite this article as: davidshotton, "Introducing the Semantic Publishing and Referencing (SPAR) Ontologies," in OpenCitations blog, 14/10/2010, https://opencitations.hypotheses.org/16.
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