Citations as First-Class Data Entities: Citation Descriptions

Requirements for citations to be treated as First-Class Data Entities

In my introductory blog post, I listed five requirements for the treatment of citations as first-class data entities.  The first of these requirements is that they must be definable in a machine-readable manner as a member of the class “Citation”, and describable using appropriate ontology terms.

This blog post describes recent additions to the OpenCitations Data Model, and to CiTO, the Citation Typing Ontology, that permit the required richer description of citations.

Changes to the OpenCitations Data Model

In the OpenCitations Data Model (OCDM), itself described in the following blog post, we have created the following new classes and properties that permit the descriptions of citations in richer ways that are appropriate for bibliometric research.  These changes have been inspired by the publications of Vincent Larivière, Ludo Waltman and their colleagues [1-3].

These new classes and properties and their definitions are described below:

New classes

  • Citation: a permanent conceptual directional link from the citing bibliographic resource to a cited bibliographic resource, created by the performative act of an author citing a published work that is relevant to the current work, typically made by including a bibliographic reference in the reference list of the citing work, or by the inclusion within the citing work of a link, in the form of an HTTP Uniform Resource Locator (URL), to the cited bibliographic resource on the World Wide Web.

The class Citation has sub-classes defining a particular type of citation.

  • Self-citation: a citation in which the citing and the cited entities have something significant in common with one another. Sub-classes include:
    • Affiliation self-citation: a citation in which at least one author from each of the citing and the cited entities is affiliated with the same academic institution.
    • Author network self-citation: a citation in which at least one author of the citing entity has direct or indirect co-authorship links with one of the authors of the cited entity.
    • Author self-citation: a citation in which the citing and the cited entities have at least one author in common.
    • Funder self-citation: a citation in which the works reported in the citing and the cited entities were funded by the same funding agency.
    • Journal self-citation: a citation in which the citing and the cited entities are published in the same journal.
  • Journal cartel citation: a citation from one journal to another journal which forms one of a very large number of citations from the citing journal to recent articles in the cited journal.
  • Distant citation: a citation in which the citing and the cited entities have nothing significant in common with one another over and beyond their subject matter.

New object properties

  • has citing document: The bibliographic resource which acts as source for the citation.
  • has cited document: The bibliographic resource which acts as target for the citation.

New data properties

  • has citation creation date:The date on which the citation was created. This has the same numerical value as the publication date of the citing bibliographic resource, but is a property of the citation itself. When combined with the citation time span, it permits that citation to be located in history.
  • has citation time span: The temporal characteristic of a citation, namely the interval between the publication date of the cited entity and the publication date of the citing entity.

Changes to CiTO, the Citation Typing Ontology

To complement these additions to the OpenCitations Data Model, and to permit these richer characteristics of citations to be encoded in RDF, we have additionally made the following changes to CiTO, the Citation Typing Ontology.

New classes

The class cito:SelfCitation has been renamed cito:AuthorSelfCitation, with an unchanged definition (“a citation in which the citing and the cited entities have at least one author in common”).

A new class cito:SelfCitation has been created, with same the more general definition as for this sub-class in the OCDM (“a citation in which the citing and the cited entities have something significant in common with one another”). In CiTO, this now includes five new sub-classes:

  • cito:AuthorSelfCitation
  • cito:JournalSelfCitation
  • cito:FunderSelfCitation
  • cito:AffiliationSelfCitation
  • cito:AuthorNetworkSelfCitation

with the definitions given above for these sub-classes in the OCDM.

New object properties

To complement the OCDM properties, we have within CiTO the following object properties:

  • cito:hasCitedEntity (“A property that relates a citation to the cited entity”) and
  • cito:hasCitingEntity (“A property that relates a citation to the cited entity”).

CiTO also has the following relevant object property:

  • cito:sharesPublicationVenueWith

with the sub-property cito:sharesJournalWith.

New data properties

To match the additions in the OCDM, we have added these new data properties to CiTO, which have the same definitions as those in the OCDM:

  • cito:hasCitationCreationDate
  • cito:hasCitationTimeSpan.

In addition, the class cito:AuthorNetworkSelfCitation is accompanied by the new data property:

  • cito:hasCoAuthorshipCitationLevel

which specifies the minimal distance that one of the authors of a citing entity has with regards to one of the authors of a cited entity according to their co-author network. For instance, a citation has a co-authorship citation level equal to 1 if at least one author of the citing entity has previously published as co-author with one of the authors of the cited entity. Similarly, we say that a citation has a co-authorship citation level equal to 2 if at least one author of the citing entity has previously published as co-author with someone who him/herself has previously published as co-author with one of the authors of the cited entity. And so on.

Describing a citation in RDF

Describing a citation between two articles in RDF as a simple link is straightforward but relatively uninformative:

<https://w3id.org/oc/corpus/br/1>
      cito:cites
          <https://w3id.org/oc/corpus/br/18> . 

The alternative RDF description of a citation as a first-class date entity could include the following triples (omitting any provenance information in this example), where br/1 and br/18 are the internal identifiers for the citing bibliographic resource and the cited bibliographic resource within the OpenCitations Corpus:

<https://w3id.org/oc/virtual/ci/1-18> a cito:Citation ;
     cito:hasCitingEntity <https://w3id.org/oc/corpus/br/1> ;
     cito:hasCitedEntity <https://w3id.org/oc/corpus/br/18> ;
     cito:hasCitationCreationDate "2016"^^xsd:gYear ;
     cito:hasCitationTimeSpan "P10Y"^^xsd:duration ;
     datacite:hasIdentifier <https://w3id.org/oc/virtual/id/ci-1-18> .

The meaning of “virtual” in the URI of this citation is explained in the following blog post about the OpenCitations Data Model.

The following diagram prepared by Silvio Peroni shows the semantic relationships for a citation currently handled by the OpenCitations Corpus (omitting the sub-classes of the class cito:Citation).  Explanation of OCI, the Open Citation Identifier, is given in a subsequent post.

References

[1]     Matthew L. Wallace, Vincent Larivière and Yves Gingras (2012. A Small World of Citations? The Influence of Collaboration Networks on Citation Practices.  PLoS ONE 7(3): e33339. https://doi.org/10.1371/journal.pone.0033339

[2]     Philippe Mongeon, Ludo Waltman and Sarah de Rijcke (2016). What do we know about journal citation cartels? A call for information.  CWTS blog post. Available at https://www.cwts.nl/blog?article=n-q2w2b4

[3]       Ludo Waltman and Caspar Chorus (2016). Journal self-citations are increasingly biased toward impact factor years. CWTS blog post. Available at https://www.cwts.nl/blog?article=n-q2x264

Cite this article as: davidshotton, "Citations as First-Class Data Entities: Citation Descriptions," in OpenCitations blog, 22/02/2018, https://opencitations.hypotheses.org/820.

‘Likes’ joins the semantic web: cito:likes

A ‘like’ button is a well-known feature in communication software such as social networking services, Internet forums, news websites and blogs that permits a user to indicate that he/she likes, enjoys or supports certain content.  Internet services that feature ‘like’ buttons usually also display the number of users who have expressed that they ‘like’ a particular item of content, providing a quantitative estimate of the strength of support for it.

In particular, the ‘Like’ button is one of Facebook’s social plug-ins, which can be use on websites outside Facebook as part of Facebook’s Open Graph.  It is valued by advertisers who wish to attract ‘likes’ for their products (and who pay Facebook for the privilege), but its use has aroused privacy concerns because it permits Facebook to track visitors to participating sites, even if they not Facebook users, giving Facebook a vast amount of information about who visits which sites.

Like it or not, however, this form of social communication has now become an integral feature of online social interactions.  For this reason, we thought it would be worthwhile to enable encoding of such ‘likes’ as open linked data, in the form of a new object property in CiTO, the Citation Typing Ontology.

This new property, cito:likes, has the following definition:

“A property that permits you to express appreciation of or interest in something, or to express that it is worth thinking about even if you do not agree with its content, enabling social media ‘likes’ statements to be encoded in RDF.  Use of this property does NOT imply the existence of a formal citation of the entity that is ‘liked’.”

An exemplar usage of cito:likes (in Turtle format) is:

sioc: <http://rdfs.org/sioc/ns#> .
foaf: <http://xmlns.com/foaf/0.1/> .
today: <http://opencitation.wordpress.com/2012/07/13/> .

today:cito-likes a sioc:Post ;
	sioc:has_creator [ 
		a sioc:UserAccount ; 
		sioc:account_of [ 
			a foaf:Person ;
			foaf:givenName "David" ;
			foaf:familyName "Shotton" ] ] .

<https://www.facebook.com/silvioperoni> a sioc:UserAccount ;
	sioc:account_of <http://www.essepuntato.it/me>;
	cito:likes today:cito-likes .

To our surprise, we found that existing ontologies did not include such a property – a search in the excellent new LOV (Linked Open Vocabularies) service revealed that no other open ontology contains the same concept as is now represented by cito:likes.

The Trait Ontology has trait:likes, but this object property has a gender-related domain, and its definition indicates that its usage is designed for expressing sexual fetish preferences.

Schema.org at first sight appears to have something resembling cito:likes, but inspection of schema:UserLike reveals this use to be specific for events.

Even the SIOC ontology, a product of the SIOC initiative (Semantically-Interlinked Online Communities) aimed at enabling the integration of online community information, which is described in an award-winning paper from DERI [1], lacks the concept ‘likes’.

So here we offer cito:likes, a property (like all other cito properties) without domain or range constraints, permitting it to be used in a wide variety of situations.

Like it? Click the Like button below!

David Shotton
Silvio Peroni

Reference

[1]     John G. Breslin, Andreas Harth, Uldis Bojars, and Stefan Decker (2005). Towards Semantically-Interlinked Online Communities.  In Proc. ESWC 2005 (A. Gómez-Pérez and J. Euzenat, Eds.); Lecture Notes in Computer Science 3532, pp. 500–514.  doi:10.1007/11431053_34.  Available from http://bit.ly/KQ2iK4.

Cite this article as: Silvio Peroni, "‘Likes’ joins the semantic web: cito:likes," in OpenCitations blog, 13/07/2012, https://opencitations.hypotheses.org/377.

Why publishers should open their references

Why should the publishers of subscription-access journals, who presently generate income from the sale of access to peer-reviewed full text scholarly articles, be willingly open the reference lists of these articles, and contribute these to the Open Citations Corpus for publication as open linked data? I would like to suggest the following reasons:

1. There is a general move towards open data, which is widely regarded as a common good. This includes citation data, i.e. bibliographic references from one article to another (in RDF Turtle format: A cito:cites B . ).
2. The reference lists at the end of journal articles are works of scholarship by the authors, who have chosen to include certain references and exclude other potentially citable papers from the reference list. However, the references themselves are simply items of bibliographic data, formatted according to the journal style, and do not benefit from the author’s creative input.
3. The reference list, together with the front matter (including the bibliographic information about the article itself) and the abstract, has traditionally been included within the copyright protection enjoyed by the article as a whole. However, the bibliographic information about the article and the article’s abstract are commonly made freely available, for example through PubMed. This same openness should now be afforded to the reference list within each article.
4. There is a home for such reference citation data: the Open Citations Corpus has been specifically created to house and publish scholarly bibliographic citation data, and is now preparing to welcome article reference lists from subscription-access journals, to supplement those already contributed from open-access journals.
5. For those publishers who already contribute their reference information to CrossRef as part of its Cited-By Linking service, this can be accomplished without any change to the publisher’s own publishing workflows, just by giving permission for CrossRef to flag the articles of certain journals as having open references. Open Citations intends to collaborate with CrossRef by harvesting the reference lists from such flagged articles, parsing them into RDF, and adding them to the Open Citations Corpus. Provided that the references are already being submitted to CrossRef, no work will have to be done by the publisher, and no changes in publishing procedure will be involved.
6. Open Citations will publish each reference list as an independent RDF Named Graph, with a unique URI, thereby protecting the integrity of the article reference list as a unit of scholarship, the source of which will be explicitly acknowledged.
7. The open citations data will then be offered back to publishers to use as they wish, e.g. for visualization of citation networks, calculation of metrics, etc., providing easier and more usable access to their own citation data than is currently afforded by commercial providers, who do not provide such data in linked data format.
8. Publishers will also be free to host their own open citations data, should they wish to do so.
9. For the majority of publishers, who would still receive subscriptions on the full articles themselves, opening their article reference lists in this way will cost nothing in terms of lost revenue.
10. Indeed, participation in the Open Citation Corpus will bring the following benefits to subscription-access publishers:
– Access to services to be built over the aggregated open citations data, for example an automated reference correction service available to editors upon receipt of a manuscript, for the automated pre-publication correction of errors in reference lists prior to article publication.
– Increased exposure to users of the references to the publisher’s own journal articles – a form of advertising. While at first coverage among subscription-access publishers will be incomplete, this expanding Open Citation Corpus will, in true Web 2.0 style, become more useful the more publishers participate.
– Even while coverage is incomplete, the Open Citations Corpus by its very nature contains reference citations to all the key papers published in every field covered – currently to all the key papers published in every biomedical field, enabling readers more easily to identify and find the most highly cited papers of each contributing publisher.
– Opening citations data will result in white-listing and general good-will from funding agencies, government and other advocates of open data, who might otherwise mandate publication by grantees in alternative open-access journals.
– Opening citations data will lead to support from scholars and researchers themselves, who wil be more inclined to publish in that publisher’s journals, feeling that at last the publishers would be giving back to them some of their own data, rather than selling it back to them as at present.

As my next blog post shows, one leading subscription-access publisher is now willing to open its journal article references in the way I have suggested.  Others who would like to so the same should contact me at <david.shotton@zoo.ox.ac.uk>.

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.

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.

Cite this article as: davidshotton, "BIBO2SPAR, an RDF Mapping of BIBO to the SPAR Ontologies," in OpenCitations blog, 29/06/2011, https://opencitations.hypotheses.org/113.

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.

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.
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