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.

 

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/.

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