As authors, we cite literature for many reasons. The reasons are normally positive:
it supports a statement we make in our article, the new work extends earlier ideas,
or the cited paper outlines a method or a dataset we use. Sometimes, however, we cite
an article differently, such as when we disagree with the conclusions from that article.
Citations help us find more information about a concept and allow individual journal
article to focus on the new content. Furthermore, they position the new work in its
historical context and citation analyses can point us to research topics we would
otherwise not have thought of [1].
Of course, citations have found additional uses that stem from the idea that articles
that are cited a lot may be important. If we assume that all citations to an article
are positive, this is a logical conclusion. However, citations are not always positive.
We can cite an article because we disagree with the statements. For example, a 2011
paper in Science about the possible inclusion of arsenate ions in DNA has seen mostly
disagreeing citations [2]. Then the article is important for a different reason.
This was picked up 10 years ago, when Shotton et al. published an ontology that formalizes
a hierarchy of reasons: the Citation Typing Ontology (CiTO, purl.org/spar/cito) [3].
This ontology defines a citation as the act of citing some article. That allows one
to make statements about the citation, in a machine readable way. Using the CiTO we
can say the citation is neutral (cito:citesAsAuthority), positive (cito:confirms),
or negative (cito:disagreesWith). The ontology also allows us to indicate reuse of
methods and software (cito:usesMethodIn) and data (cito:usesDataFrom). This, of course,
is closely related to recent efforts in data citation [4] and software citation [5].
The adoption of the CiTO, however, has so far not been wide in publishing. CiteULike
[6] was one of the first tools that had support [7]. It allowed users to create citations
with CiTO typing (see Fig. 1).
Fig. 1
Screenshot of CiteUlike showing the citation between two articles and that the reason
is that the citing article uses the method proposed in the cite article (cito:usesMethodIn)
Adopting the CiTO
If the past 10 years has shown anything, it is that the activity of scholarly communication
via journal articles is not easily changed. Whether it is widespread adoption of data
repository, minimal reporting standards, or freely sharing citations, the interest
may be there, but the uptake is slow. The OpenCitations project [8, 9] and Initiative
for Open Citations [10] show how hard it is to change the momentum. And while CiteULike
introduced support for the CiTO, other references managers have not (yet). A chicken-and-egg
situation may be an underlying issue: if there are no providers of CiTO annotation,
why should tools that work with citations use it? And at the same time, if there is
no use of it, why invest effort to provide such annotation.
However, the Journal of Cheminformatics considers adoption important. For example,
we may want to learn what articles are using a method proposed in some article. We
may want to see how data is reused, or we may want to get warned that we are citing
an article that has been refuted repeatedly.
Therefore, we are starting a pilot to roll out CiTO annotation in the Journal of Cheminformatics.
We take advantage here of the ability to add notes to full form (see [3]) references
in bibliographies. These are referred to as bibnotes. The content of the note will
be strictly formatted: it will use the syntax [
cito:usesMethodIn
] and formatted in bold. That is, the bibnote starts with the [ character, followed
by one of the CiTO types, and ending with the ] character. If you wish to provide
more than one annotation, you can repeat this syntax, separated by one or more spaces,
for example: [
cito:usesMethodIn
]
[
cito:citeAsAuthority
]. By using this specific syntax, we introduce a level of machine readability such
that this annotation can be extracted with text mining approaches and used by downstream
citation projects.
These bibnotes can be used to overwrite the default cito:cites. We currently encourage
authors interested in participating in this pilot to use the following CiTO types:
cito:citesAsDataSource when you use data in your paper from the cited source, cito:usesMethodIn
when you use a method from the cites source, cito:citesAsAuthority for articles that
you cite as authorative works in the field, cito:discusses when you discuss the content
of the cited article, and cito:extends when your article describes a new release of
software or database described in the cited article. However, you are free to use
any of the other CiTO types, including cito:agreesWith and cito:disagreesWith.
We also plan to adopt this approach for comments (cito:repliesTo) and errata/corrigenda/corrections
(cito:updates). These annotations will be handled at an editorial level.
With this pilot we hope to trigger further adoption of approaches like CiTO. We plan
to use this information in WikiCite [11] and Scholia [12] to demonstrate downstream
use, but hope that projects like OpenCitations and SciGraph (www.springernature.com/gp/researchers/scigraph)
will pick it up too. During the pilot, we will also develop practical guidance on
how to use reference managers and type setting tools like Microsoft Word and LaTeX
can be used to add these annotations.
Let this be the egg or chicken (depending on your philosophy), we are looking to innovate
how we cite our literature.