=Paper=
{{Paper
|id=Vol-1282/paper6
|storemode=property
|title=Semantic Lenses to Bring Digital and Semantic Publishing Together
|pdfUrl=https://ceur-ws.org/Vol-1282/lisc2014_submission_6.pdf
|volume=Vol-1282
|dblpUrl=https://dblp.org/rec/conf/semweb/IorioPVZ14
}}
==Semantic Lenses to Bring Digital and Semantic Publishing Together==
https://ceur-ws.org/Vol-1282/lisc2014_submission_6.pdf
Semantic lenses
to bring digital and semantic publishing together
Angelo Di Iorio1 , Silvio Peroni1,2 , Fabio Vitali1 , and Jacopo Zingoni1
1
Department of Computer Science and Engineering, University of Bologna (Italy)
{angelo.diiorio, silvio.peroni, fabio.vitali, jacopo.zingoni}@unibo.it
2
STLab-ISTC, Consiglio Nazionale delle Ricerche (Italy)
Abstract. Modern scholarly publishers are making steps towards se-
mantic publishing, i.e. the use of Web and Semantic Web technologies to
represent formally the meaning of a published document by specifying
information about it as metadata and to publish them as Open Linked
Data. In this paper we introduced a way to use a particular seman-
tic publishing model, called semantic lenses, to semantically enhance a
published journal article. In addition, we present the main features of
TAL, a prototypical application that enables the navigation and under-
standing of a scholarly document through these semantic lenses, and we
describe the outcomes of a user testing session that demonstrates the
efficacy of TAL when addressing tasks requiring deeper understanding
and fact-finding on the content of the document.
Keywords: Web interface, document semantics, semantic publishing
1 Introduction
Simultaneously to the evolution of the Web by means of Semantic Web tech-
nologies, modern publishers (and in particular scholarly publishers) are making
steps towards the enhancing of digital publications with semantics, an approach
that is known as semantic publishing [22]. In brief, semantic publishing is the
use of Web and Semantic Web technologies to represent formally the meaning
of a published document by specifying a large quantity of information about
it as metadata and to publish them as Open Linked Data. As a confirmation
of this trend, recently the Nature Publishing Group (publisher of Nature), the
American Association for the Advancement of Science (publisher of Science) and
the Oxford University Press have all announced initiatives to open their articles’
reference lists and to publish them as Open Linked Data3,4,5 .
3
Nature.com Linked Data: http://data.nature.com.
4
http://opencitations.wordpress.com/2012/06/16/science-joins-nature-in-opening-
reference-citations
5
http://opencitations.wordpress.com/2012/06/22/oxford-university-press-to-
support-open-citations
However, the enhancement of a traditional scientific paper with semantic an-
notations is not a straightforward operation, since it involves much more than
simply making semantically precise statements about named entities within the
text. In [17], we have shown how several relevant points of view exist beyond
the bare words of a scientific paper – such as the context of the publication, its
structural components, its rhetorical structures (e.g. Introduction, Results, Dis-
cussion), or the network of citations that connects the publication to its wider
context of scholarly works. These points of view are usually combined together
to create an effective unit of scholarly communication so well integrated into the
paper as a whole and into the rhetorical flow of the natural language of the text,
so as to be scarcely discernible as separate entities by the reader. We also pro-
pose the separation of these aspects into eight different sets of machine-readable
semantic assertions (called semantic lenses), where each set describes one of
(from the most contextual to the most document-specific): research context, au-
thors’ contributions and roles, publication context, document structure, rhetoric
organisation of discourse, citation network, argumentative characterisation of
text, and textual semantics.
How can the theory of semantic lenses be used to extend effectively seman-
tic publishing capabilities of publishers? In order to provide an answer to this
question, in this paper we introduce a prototypical HTML interface to scholarly
papers called TAL (Through A Lens), which enables the navigation of a text
document on which semantic lenses have been applied to make explicit all the
corresponding information. This HTML interface is meant to be a proof of con-
cept of the semantic lenses in a real-case scenario. We performed a user testing
session that demonstrates the efficacy of TAL when addressing tasks requiring
deeper understanding and fact-finding on the content of the document.
The rest of the paper is organised as follows. In Section 2 we introduce
some significant works related to semantic publishing experiences and models. In
Section 3 we show an application of semantic lenses onto a particular scholarly
article. In Section 4 we introduce TAL describing its main features, while in
Section 5 we discuss the outcomes of a user testing session we performed to
assess the usability and effectiveness of TAL. Finally (Section 6) we conclude
the paper sketching out some future works.
2 Related works
Much current literature concerns both the proofs of concepts for semantic pub-
lishing applications and the models for the description of digital publishing from
different perspective. Because of this richness, here we present just some of the
most important and significant works on these topics.
In [22], Shotton et al. describe their experience in enriching and providing ap-
propriate Web interfaces for scholarly papers enhanced with provenance informa-
tions, scientific data, bibliographic references, interactive maps and tables, with
the intention to highlights the advantages of semantic publishing to a broader
audience. Along the same lines, in their work [19] Pettifer et al. introduce pros
and cons of the various formats for the publication of scholarly articles and pro-
pose an application for the semantic enhancement of PDF documents according
to established ontologies.
A number of vocabularies for the description of research projects and related
entities have been developed, e.g. the VIVO Ontology6 – developed for describing
the social networks of academics, their research and teaching activities, their
expertise, and their relationships to information resources –, the Description
Of A Project7 – an ontology with multi-lingual definitions that contains terms
specific for software development projects – and the Research Object suite of
ontologies [1] – for linking together scientific workflows, the provenance of their
executions, interconnections between workflows and related resources (datasets,
publications, etc.), and social aspects related to such scientific experiments.
One of the most widely used ontology for describing bibliographic entities
and their aggregations is BIBO, the Bibliographic Ontology [3]. FRBR, Func-
tional Requirements for Bibliographic Records [10], is yet another more struc-
tured model for describing documents and their evolution in time. One of the
most important aspects of FRBR is the fact that it is not tied to a particular
metadata schema or implementation.
Several works have been proposed in the past to model the rhetoric and
argumentation of papers. For instance, the SALT application [9] permits someone
such as the author “to enrich the document with formal descriptions of claims,
supports and rhetorical relation as part of their writing process”. There are
other works, based on [23], that offer an application of Toulmin’s model within
specific scholarly domains, for instance the legal and legislative domain [11].
A good review of all the others Semantic Web models for the description of
arguments can be found in [21].
3 The Semantic Lenses
In [17], we claimed that the semantics of a document is definable from different
perspectives, where each perspective is represented as a semantic lens that is
applied to a document to reveal a particular semantic facet. In this section we
briefly summarise our theory. A full example of the lenses applied to a well-known
paper Ontologies are us: A unified model of social networks and semantics [14]
is available at http://www.essepuntato.it/lisc2014/lens-example.
Lenses are formalised in the LAO ontology8 . In addition, since the application
of the semantic lenses to a document is an authorial activity, i.e. the action of
a person (the original author as well as anyone else) taking responsibility for a
semantic interpretation of the document, we also record the provenance of the
semantic statements according to the Provenance Ontology (PROV-O) [12].
Figure 1 summarises the overall conceptual framework. The lenses are organ-
ised in two groups: context-related, which describe the elements contributing to
6
VIVO Ontology: http://vivoweb.org/ontology/core
7
DOAP: http://usefulinc.com/ns/doap
8
Lens Application Ontology (LAO): http://www.essepuntato.it/2011/03/lens.
Fig. 1. The layout of Semantic Lenses in relation to the facets of a scientific document.
the creation and development of a paper, and content-related, which describe
the content itself of the paper from different angles.
3.1 Describing the context
Writing a scientific paper is usually the final stage of an often complex collabo-
rative and multi-domain activity of undertaking the research investigation from
which the paper arises. The organizations involved, the people affiliated to these
organizations and their roles and contributions, the grants provided by funding
agencies, the research projects funded by such grants, the social context in which
a scientific paper is written, the venue within which a paper appears: all these
provide the research context that leads, directly or indirectly, to the genesis of
the paper, and awareness of these may have a strong impact on the credibility
and authoritativeness of its scientific content.
Three lenses are designed to cover these aspects:
– Research context: the background from which the paper emerged (the re-
search described, the institutions involved, the sources of funding, etc.). To
describe such contextual environment we use FRAPO, the Funding, Research
Administration and Projects Ontology9 .
– Contributions and roles: the individuals claiming authorship on the paper
and what specific contributions each made. We use SCoRO (the Scholarly
Contributions and Roles Ontology10 ) and its imported ontology PRO (the
Publishing Roles Ontology11 ) [18] to describe these aspects.
9
FRAPO: http://purl.org/cerif/frapo
10
SCoRO: http://purl.org/spar/scoro
11
PRO: http://purl.org/spar/pro
– Publication context: any information about the event (e.g., a conference) and
publication venue of the paper (such as the proceedings or the journal), as
well as connections to the other papers sharing the same event or venue. This
part is described by using FaBiO, the FRBR-aligned Bibliographic Ontology12
[16] and BiRO, the Bibliographic Reference Ontology13 [5].
Note that all the ontologies used or suggested in this paper to describe
“lenses” statements have been chosen as an appropriate and convincing exam-
ple of an ontology that fulfils the requirements for the lens, since they allow us
to fully describe all the document aspects we are interested in. However, their
use is not mandatory, so as to leave people to use other models (such as those
described in Section 2) instead of them.
3.2 Describing the content
The semantics of the content of a document, i.e. such a semantics that is implic-
itly defined in and inferable from the text, can be described from different points
of view. For example, the semantical structure of the text – i.e. the organization
of the document as structured containers, blocks of text, inline elements – is
often expressed by means of markup languages such as XML and LaTeX, that
have constructs for describing content hierarchically.
In a Semantic Web context, we would rather use an ontology that describes
the markup structures in OWL. For this reason, we use EARMARK [8], an on-
tology14 of a markup metalanguage, to describe the structure of the document as
a set of OWL assertions to associate formal and explicit semantics [15]. Through
the Pattern Ontology (PO)15 [6] in combination with EARMARK we can asso-
ciate a particular structural semantics to markup elements, such an element h1
expressing the concept of being a block of text, or the div element containing it
being a container. This is covered by the document structure lens.
Close to that, we place the identification and organization of the rhetorical
components of the text, such as a section being an Introduction, some para-
graphs describing the Methods of the research, or the presented Results or the
paper’s Conclusion), in order to label all the meaningful aspects of the scientific
discourse. Such rhetoric characterization of markup structures can be specified
through DoCO, the Document Components Ontology16 , and DEO, the Discourse
Elements Ontology17 .
In addition, strictly correlated with the rhetorical aspects of a document,
we can detail the organization of the claims and the arguments of the paper
(providing evidences to a claim).The argumentative organisation of discourse is
12
FaBiO: http://purl.org/spar/fabio
13
BiRO: http://purl.org/spar/biro
14
EARMARK: http://www.essepuntato.it/2008/12/earmark
15
PO: http://www.essepuntato.it/2008/12/pattern
16
DoCO: http://purl.org/spar/doco
17
DEO: http://purl.org/spar/deo
described using AMO, the Argument Model Ontology18 , that implements Toul-
min’s model of argumentation [23]19 in OWL.
The textual semantics, i.e. the very message contained in a piece of text, is
the final step in the definition of the semantics of a piece of text. For instance,
the formal description of a claim needs to be expressed in such a way as to
represent as faithfully as possible the meaning of the claim itself. Since each
document expresses content in domains that are specific of the topic of the
paper, we cannot provide an encompassing ontology to express claims. In some
cases, the claim of an argument can be encoded through using a simple model,
e.g. DBPedia.
Finally, a document takes also part to a citation network with its cited doc-
uments, in particular taking into account the reasons for particular citations –
e.g. to express qualification of or disagreement with the ideas presented in the
cited paper – which may effect the evaluation of a citation network itself. Using
CiTO, the Citation Typing Ontology20 [16], we provide descriptions of the nature
of the citations.
4 Application of the theory
In this section we provide an answer to the question we introduced in Section 1
– how can the theory of semantic lenses be used to extend effectively semantic
publishing capabilities of publishers?
We look at this issue from two orthogonal points of view: (i) identifying the
actors involved in the process and (ii) presenting a tool to help readers to focus
on distinct aspects of the same document so as to benefit from ‘lenses-based’
semantic annotations.
4.1 Authoring Semantic Lenses
The application of any particular lens to a document is an authorial operation
in the sense that is an act involving individuals acting as agents, responsible for
the choice of determined semantic interpretations on a document or its content.
Although it seems to be necessary to have authors involved in the application
of semantic lenses, thus tracking the provenance of semantic assertions of an
enriched document, it may be more difficult and even unclear to understand the
possible relationship between the authorship of semantic lenses and the actors
involved in that authorship. Semantic Publishing involves different actors of
18
AMO: http://www.essepuntato.it/2011/02/argumentmodel
19
Toulmin proposed that arguments are composed of statements having specific argu-
mentative roles: the claim (a fact that must be asserted), the evidence (a foundation
for the claim), the warrant (a statement bridging from the evidence to the claim),
the backing (credentials that certifies the warrant), the qualifier (words or phrases
expressing the degree of certainty of the claim) and the rebuttal (restrictions that
may be applied to the claim).
20
CiTO: http://purl.org/spar/cito
the publication chain [22] – such as authors, reviewers, editors and publishers
– who may be responsible for the application of particular kinds of metadata
rather than others. Within the semantic lenses domain, it is quite important to
identify how all these actors are involved in the application of semantic lenses.
Of course, there is no clear-cut answer to this question, but based on our own
experience in field-testing the application of lenses, we find reasonable to suggest
some guidelines, beginning by considering how much the original authors of the
document might be involved in the generation of semantic lenses. In Table 1 we
summarise our own findings and recommendations about the involvement of the
authors or other possible actors that might intervene on each semantic lens.
Table 1. Summary of suggested involvement in the authoring of lenses.
Semantic Author
Other actors usually involved
lens involvement
Publisher: can specify additional semantics to text (e.g., the abstract).
Proof reader: detects errors prior to final publication and can propose
Highly
Semantics appropriate changes.
recommended
Reader: can provide a semantic interpretation of author’s text such as in
form of nanopublication.
Highly
Argumentation Reviewer: can suggest different way of presenting and defending a claim.
recommended
Publisher: can expand the citation network of the document according to
implicit and/or inferable relations, e.g., links to related papers and so on.
Reader: can link the article in unpredictable way according to his/her own
Citation Recommended
interests, also with auxiliary application such as CiteULike
Reviewer: can propose additional citation links between the document in
consideration and related materials according to particular reasons
Editor: can provide semantics of the particular rhetoric organisation of
sections so as to conform the document in consideration to the proposed
Rhetoric Recommended organisation of a particular journal.
Reader: can enhance particular blocks of text so as to make explicit the
perceived rhetoric of such a text, e.g. for future searches.
Publisher: can suggest and/or apply a different structural organisation of
Structure Limited
the text according to publishing formats and needs.
Editor and publisher: provide contextual information about the actual
Publication
Not required venue where the document was published and how it appears within
context
bibliographic reference lists of other papers.
Contributions Publisher: can complete the information provided by authors about their
Recommended
and roles contributions and roles within the document in consideration.
Funding agency and institution: can provide additional metadata to
Research Highly
describe their involvement related to the document and, thus, to increase
context recommended
their visibility within the Web of Data.
Even if we have broadly identified author’s involvement and other actors
in semantic lenses applications, the time when one can apply these lenses can
vary. On the one hand, the timeframe for the application of the context-specific
lenses relates to several aspects that may be gathered only after the document
publication (e.g., the publication venue, the DOI, etc.). On the other hand,
according to the other content-specific lenses, there is the possibility to apply
them within the same timeframe of the document creation, since the author’s
involvement would be more straightforward. As a result the information would
arguably be far more accurate than a post-hoc application.
However, the above ideal approach does not address some fundamental tech-
nical issues. First, it supposes that authors already know how to apply semantic
lenses, or could become quickly familiar with semantic lenses, their definitions,
and concepts and meanings encoded by the ontologies used. In addition, the
application of semantic lenses requires a good amount of technical knowledge,
which is an unreasonable expectation for non-experts. In the next section we
propose a solution for helping users understanding semantic lenses.
4.2 Through A Lens
The knowledge of the languages used to represent lens-related semantic data
is crucial to understand and use semantic lenses appropriately. This knowledge
seems to be the most significative obstacle to a wide adoption of semantic lenses,
since several actors (e.g. publishers, readers, authors) may not be experts of such
semantic technologies. A common solution is to hide the intrinsic complexities of
such technologies behind an interface that allows anyone (even the non-expert) to
use a tool like semantic lenses in an easy way. To this end, we developed a proto-
typical HTML interface to scholarly papers called TAL (Through A Lens), which
enables the navigation of a text document on which semantic lenses have been
applied to make explicit all the corresponding information. As input, TAL takes
an EARMARK representation [8] of a document – we use an HTML version of
[14] in the online-available prototype21 – properly enriched with lens-related se-
mantic assertions as shown in Section 3. The production of annotated documents
is not simple. EARMARK includes a Java API on top of which we are developing
sophisticated editors. At this stage, we used that API to annotate the sample
document. Further developments on the authoring of semantic-lenses-enabled
documents are still needed. TAL generates an HTML page with the article and
some tools enabling a quick and smart navigation.
Argumentation index. This index is generated from semantic data re-
lated to the argumentation lens. It lists all the argumentations of the document,
making possible to click on each claim within this index to scroll the document
down to where the sentence of the claim is written and to show up the related
argumentative components (evidences, warrants, backings, qualifiers and rebut-
tals). Figure 2.A shows a TAL screenshot with this summary. Claim seven is
expanded, others are left unexpanded. Each type of component of a claim (e.g.
Evidence, Warrant, Backing, etc.) is explicitly labeled, and coloured in a way to
be immediately distinguishable from other types.
Rhetoric Denotation. Labels are placed at the beginning of each paragraph
to mean its rhetoric function according to data related to the rhetoric lens. Figure
2.B contains the rhetoric denotation of a paragraph.
21
http://www.essepuntato.it/lisc2014/LensedMika.html
Fig. 2. Three TAL screenshots showing: (A) the argumentation index, (B) a rhetoric
denotation of a paragraph, and (C) the citation index with the tooltip box.
Citation index. This index is the counterpart of the argumentation index,
but realised over the citation lens. The purpose is to give an interactive table
of content for the whole set of citations made by the document, and to offer a
level of readability and interactivity similar to the one seen in the argumentation
index, by explicitly showing all the citations within the text, grouped by their
related CiTO properties and ordered by frequency in the document, together
with pointers to their occurrences within the text. An example is shown in
Figure 2.C. The position and the way to open the citation index is the same
of the argumentation one. Once it expands, the summary reveals a first list of
CiTO properties. This list is ordered by frequency of use within the document.
Clicking on a property, a nested sub-list is unfolded with the references to all
citation items exhibiting that property. To each item is associated a summary
of the bibliographic reference information originally contained within the text,
together with pointers to both the complete bibliographic reference, as well as
anchor links to each occurrence of the citation within the document.
Tooltip box. A yellow box, shown in Figure 2.C, is placed on the right
side of the document content. It will be used to show additional information
about in-line references (such as the factual or rhetoric reason of citations) and
claims (such as the rhetoric denotation of paragraphs containing them) when
hovering them with the mouse pointer. All the information visualised in the box
are generated starting from semantic data related to the lenses argumentation,
citation and rhetoric.
5 Experiment and evaluation
At this stage of the development of the TAL prototype, we undertook user test-
ing on it, not solely to gather data about its usability and effectiveness, but
mostly to probe if the road we had undertaken in order to make available our
set of lens browsing features might be potentially promising. We asked 9 subjects
with different backgrounds (Ph. D. students and people working in publishing
houses) to perform three unsupervised tasks (max. 5 minutes per task), involving
navigation of Mika’s paper [14] through TAL. There were no “administrators”
observing the subjects while they were undertaking these tasks. All the subjects
were volunteers who responded to personal e-mails. When prototype develop-
ment will be over, we plan to execute further user tests, including comparative
ones, and with a larger user base.
The tasks given to the subjects are shown in Table 2. This set of tasks was
designed to exploring the TAL capabilities in enabling an intuitive and useful
navigation of papers. The test session was structured as follows. Firstly, as a
warm-up task, we asked subjects to use TAL to find the paragraph containing the
second claim and to write down all the citations in that paragraph, explaining
also the reason for the citation (max. 5 minutes). Then, as the real test, we
asked subjects to complete the three tasks listed in Table 2 using TAL (max. 5
minutes per task). Finally, we asked subjects to fill in two short questionnaires,
one multiple choice and the other textual, to report their experience of using
TAL to complete these tasks (max. 10 minutes). All the questionaries and all
the outcomes of the experiments are available online22 .
Table 2. The three tasks subjects performed in the user testing session.
Task 1 Write down all the reasons why the document cites the reference [8]
Write down the evidences of the claim “It is important to note that in terms of knowledge
Task 2 representation, the set of these keywords cannot even be considered as vocabularies, the
simplest possible form of an ontology on the continuous scale of Smith and Welty [5]”
Write down the (first words of the) paragraphs containing statements of the problems
Task 3
discussed in the paper
Out of 27 tasks in total (3 tasks given to each of 9 subjects), 20 were com-
pleted successfully (i.e., the right answers were given), while 7 had incorrect or
incomplete answers, giving an overall success rate of 74%. The 20 successes were
distributed as follows: 5 in Task1, 9 in Task2 and 6 in Task3.
The usability score for TAL was computed using the System Usability Scale
(SUS) [2], a well-known questionnaire used for the perception of the usability of a
22
http://www.essepuntato.it/lisc2014/questionaries
system. In addition to the main SUS scale, we also were interested in examining
the sub-scales of pure Usability and pure Learnability of the system, as proposed
recently by Lewis and Sauro [13]. As shown in Table 3, the mean SUS score for
TAL was 70 (in a 0 to 100 range), surpassing the target score of 68 to demonstrate
a good level of usability [20]. The mean values for the SUS sub-scales Usability
and Learnability were 69.44 and 72.22 respectively.
Table 3. SUS values and related sub-measures.
Measure Mean Max. value Min. value S. deviation
SUS value 70 95 50 13.58
Usability 69.44 93.5 53.13 12.18
Learnability 72.22 100 37.5 24.83
6 Conclusions
Modern publishers are now approaching digital publishing from a semantic per-
spective, making steps towards semantic publishing. In this paper we introduce
a way to use semantic lenses [17] to semantically enhance a published journal
article. In addition, we also introduced TAL, a prototypical application we de-
veloped as proof of concept of the use of semantic lenses in a real-case scenario,
that enables the navigation and understanding of a scholarly document through
these semantic lenses. Although TAL is still a prototype rather than a complete
application, the outcomes reported from the user testing session were positive
and very encouraging. In the future we plan to extend TAL so as to handle ad-
ditional ways of navigation according to all the eight lenses introduced, as well
as to produce semantic assertions according to each lens through automatic or
semi-automatic approaches, as already proposed for the structural lens [6, 7] and
the citation lens [4].
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