Graffoo, a Graphical Framework for OWL Ontologies

Graffoo, a Graphical Framework for OWL Ontologies [1], is a wonderful new open source tool developed by Silvio Peroni that can be used to present the classes, properties and restrictions within OWL ontologies, or sub-sections of them, as clear and easy-to-understand diagrams. Several Graffoo diagrams have been developed to explain SPAR ontologies, or portions of them, and are to be found in the appropriate ontology directories at https://sempublishing.svn.sourceforge.net/svnroot/sempublishing/.

For example, in Figure 1 the diagram, BiRO.png, illustrates the structure of BiRO, the Bibliographic Reference Ontology:


Graffoo diagram of BiRO, the Bibliographic Reference Ontology

The upper part of this diagram shows how a bibliographic record, which in FRBR terminology is a Work, (a) is a set of components (author names, publication year, title, volume number, ISSN, publisher, dates of submission, acceptance and publication, etc.), (b) references a published entity (a FRBR Endeavor), and (c) can form part of a bibliographic collection such as a library catalogue, which is also a set of components, in this case of bibliographic records.

The lower part of the diagram shows how such a bibliographic record can be realized (i.e. expressed in a specific form, forming what in FRBR terminology is an Expression) as a bibliographic reference, such as you might find in an article’s reference list. The bibliographic reference, while referencing the same published entity, differs from a bibliographic record in two important ways.

  • First, a bibliographic reference typically does not include all the components of the full bibliographic record. References typically exclude the ISSN, the name of the publisher, and the submission and acceptance dates; may exclude the publication date and some of the authors’ names if there are many authors; and in certain journal (e.g. Nature) also exclude the title.
  • Second, the components of a bibliographic reference form an ordered list rather than a set, although the precise order of components can vary from journal to journal (e.g. whether or not the publication year immediately follows the authors’ names).

The diagram also shows that, just as bibliographic records may be grouped into bibliographic collections, so bibliographic references may be grouped into bibliographic lists such as reference lists (which, of course, are themselves ordered lists), nicely exposing the symmetry within the BiRO ontology in a manner that would be hard to grasp simply by looking at the class structure within an ontology editor such as Protégé.

The advantages of using such a Grafoo diagram are thus that it displays the logical relationships between elements of an ontology, or a sub-section of an ontology, in a manner that is relatively straightforward to understand, once one has grasped the meaning of the different elements of a Graffoo diagram. These elements are shown and defined in the Graffoo key (Figure 2).

Figure 2: The legend for all possible Graffoo objects

From our preliminary empirical studies, it appears that Graffoo allows us to create representations of OWL ontologies that can be comprehended in detail without the person viewing them having to understand the details of OWL 2 or of any of its linearizations (Turtle, RDF/XML, Manchester Syntax, or OWL/XML).

Graffoo has been developed using the standard library of the yEd diagram editor, a free diagram editor running on Windows, Mac and Linux. The graphml format version of those Graffoo objects is also available here. We commend the use of Graffoo to other ontologists.

[1] Graffoo, the Graphic framework for OWL ontologies. http://www.essepuntato.it/graffoo.

Cite this article as: davidshotton, "Graffoo, a Graphical Framework for OWL Ontologies," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/71.

Using LODE for ontology visualization

Silvio Peroni has recently created LODE (Live OWL Documentation Environment; http://lode.sourceforge.net/), a new ontology visualization service that automatically extracts classes, object properties, data properties, named individuals, annotation properties, general axioms and namespace declarations from an OWL or OWL2 ontology, and renders them as ordered lists, together with their textual definitions, in a human-readable HTML page designed for browsing and navigation by means of embedded links.  The Cascading Style Sheets used for this page are based on the W3C CSSs for Recommendation documents.

This LODE service is an open source development, and can be freely used, as described at http://lode.sourceforge.net/. It may be used in conjunction with content negotiation to display the human-readable LODE version of an OWL ontology when the user accesses the ontology using a web browser, or alternatively to deliver the OWL ontology itself when the user accesses the ontology using an ontology editing tool such as Protégé and NeOn Toolkit.  It is in this way that LODE is being employed to visualize the SPAR (Semantic Publishing and Referencing) Ontologies (http://purl.org/spar/).

Cite this article as: davidshotton, "Using LODE for ontology visualization," in OpenCitations blog, 25/02/2011, https://opencitations.hypotheses.org/62.

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.

Using CiTO in WordPress

In his recent blog post entitled How to use Citation Typing Ontology (CiTO) in your blog posts, Martin Fenner describes a plug-in for WordPress he has created that makes it easy to add citation typing into your blog post, using a sub-set of the CiTO (Citation Typing Ontology) relationships presented in a convenient drop-down menu.  Full details at http://blogs.plos.org/mfenner/2011/02/14/how-to-use-citation-typing-ontology-cito-in-your-blog-posts/.   Many thanks, Martin!

Cite this article as: davidshotton, "Using CiTO in WordPress," in OpenCitations blog, 25/02/2011, https://opencitations.hypotheses.org/1044.

How to employ CiTO in CiteULike

Jodi Schneider of DERI has posted on her blog at http://jodischneider.com/blog/2010/10/18/cito-in-the-wild/ a most helpful description of how to employ CiTO properties characterizing bibliographic citations as tags for references in CiteULike.

Thanks, Jodi!

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Use of CiTO in CiteULike

Egon Willighagen, at Uppsala University, has pioneered the use of object properties from CiTO, the Citation Typing Ontology, to characterize bibliographic citations in CiteULike, the free service for managing and discovering scholarly references.  Indeed, it was his use case that persuaded me of the need to generalize CiTO to include indirect citations.

For example, in documenting papers that use the Chemistry Development Kit (CDK), Egon records the following paper by Guha (2007) (Egon’s CiteULike reference 7901082): 

He tags that Guha paper, using the CiTO tag cito:usedMethodIn, as using the CDK method described in a paper by Steinbeck et al. (2003) (Egon’s CiteULike reference 423382):

However, the original paper by Guha that has been tagged by Egon does not cite  Steinbeck et al. (2003) directly in its reference list.  Rather, it contains a reference to a later paper on CDK by Steinbeck et al. (2006), entitled “Recent developments of the Chemistry Development Kit (CDK)” (Egon’s CiteULike reference 1073448):

. . . , a paper that Egon tags as extending the original 2003 paper describing CDK, using the property cito:extends.

Thus the Guha paper cites Steinbeck et al. (2003) only indirectly, via Steinbeck et al. (2006).  For this reason, the scope of CiTO was extended to include such indirect citations.  The description of CiTO now reads:

“The purpose of the CiTO Ontology is to enable characterization of the nature or type of citations, both factually and rhetorically.  The citations characterized may be either direct and explicit (as in the reference list of a journal article), indirect (e.g. a citation to a more recent paper by the same research group on the same topic), or implicit (e.g. as in artistic quotations or parodies, or in cases of plagiarism).”

Thanks, Egon!

Cite this article as: davidshotton, "Use of CiTO in CiteULike," in OpenCitations blog, 21/10/2010, https://opencitations.hypotheses.org/31.

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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