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Hyperlink DOIs to preferred resolver #3

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2 changes: 1 addition & 1 deletion mediatype/index.html
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Expand Up @@ -52,7 +52,7 @@ <h1 class="featurette-heading">
<li><p><a href="https://w3id.org/spar/mediatype/text/turtle.html">.html</a> for having the data in HTML.</p></li>
</ul>
<p>All these resources defining media types can be used for specifying particular formats (e.g., by means of the DCTerms property <a href="http://purl.org/dc/terms/format">dcterms:format</a>) that a certain entity, such as a book or a dataset, can have. In the <a href="http://www.sparontologies.net/ontologies/fabio">FRBR-align Bibliographic Ontology (FaBiO)</a>, the specification of such format is a typical information associated to the manifestation level (i.e., <a href="http://purl.org/spar/fabio/Manifestation">fabio:Manifestation</a>) of an entity.</p>
<p>A dump of all these data is available on <a href="http://dx.doi.org/10.6084/m9.figshare.1608294">figshare</a>.</p>
<p>A dump of all these data is available on <a href="https://doi.org/10.6084/m9.figshare.1608294">figshare</a>.</p>
<p>Please do not hesitate to <a href="mailto:[email protected]?subject=About the LOD dataset on media types&body=Dear Silvio,%0D%0D[Please write here your text.]">contact us</a> for questions and additional information about this LOD dataset.</p>
</div>

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4 changes: 2 additions & 2 deletions spar/about.html
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Expand Up @@ -85,9 +85,9 @@ <h3><a class="anchor" id="genesis"></a>
</span>
</h3>
<p>The original motivation for creating the first of these ontologies, the <a href="/ontologies/cito">Citation Typing Ontology (CiTO)</a>, was provided by the semantic publishing work undertaken in 2008, described in:</p>
<p class="bg-info cite">Shotton, D., Portwin, K., Klyne, G., Miles, A. (2009). Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. In PLoS Computational Biology, 5(4): e1000361. <a href="http://dx.doi.org/10.1371/journal.pcbi.1000361">http://dx.doi.org/10.1371/journal.pcbi.1000361</a></p>
<p class="bg-info cite">Shotton, D., Portwin, K., Klyne, G., Miles, A. (2009). Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. In PLoS Computational Biology, 5(4): e1000361. <a href="https://doi.org/10.1371/journal.pcbi.1000361">http://dx.doi.org/10.1371/journal.pcbi.1000361</a></p>
<p>The version 1.6 of the CiTO ontology was developed by <a href="http://www.oerc.ox.ac.uk/people/david-shotton">David Shotton</a> from that work and published in 2009 in the following paper:</p>
<p class="bg-info cite">Shotton, D. (2010). CiTO, the Citation Typing Ontology. In Journal of Biomedical Semantics, 1 (Suppl 1):S6. <a href="http://dx.doi.org/10.1186/2041-1480-1-S1-S6">http://dx.doi.org/10.1186/2041-1480-1-S1-S6</a></p>
<p class="bg-info cite">Shotton, D. (2010). CiTO, the Citation Typing Ontology. In Journal of Biomedical Semantics, 1 (Suppl 1):S6. <a href="https://doi.org/10.1186/2041-1480-1-S1-S6">http://dx.doi.org/10.1186/2041-1480-1-S1-S6</a></p>
<p>In the second half of 2010, <a href="http://www.essepuntato.it">Silvio Peroni</a>, a Ph.D. student at that time, came for six months as an intern from the <a href="http://www.unibo.it">University of Bologna</a> to <a href="http://www.zoo.ox.ac.uk/people/view/shotton_dm.htm">David's research group at the University of Oxford</a>. In those six months, Silvio and David separated out from CiTO those aspects describing bibliographic entities into <a href="/ontologies/fabio">FaBiO</a>, the FRBR-aligned Bibliographic Ontology, those aspects describing the quantification of citations into <a href="/ontologies/c4o">C4O</a>, the Citation Counting and Context Characterization Ontology, and those aspects describing the status of publications into <a href="/ontologies/pso">PSO</a>, the Publications Status Ontology, leaving the current version of <a href="/ontologies/cito">CiTO</a> (v2) with the sole role of describing the nature and character of the citations themselves. In addition, during that time, they worked intimately and intensely together in a way that was remarkable and mutually beneficial, developing a unique corpus of new work relating to Semantic Publishing, i.e., the <a href="/ontologies">Semantic Publishing and Referencing (SPAR) Ontologies</a>.</p> <p>Following Silvio's return to Bologna, they continued to collaborate actively. Their actual corpus of work includes new ontologies that are finding <a href="/uptake">increasing use worldwide</a>, tools to assist third parties in the creation of ontologies (e.g., <a href="http://www.essepuntato.it/lode">LODE</a> and <a href="http://www.essepuntato.it/graffoo">Graffoo</a>), and mappings of document markup and metadata standards to RDF (e.g., <a href="http://www.ncbi.nlm.nih.gov/books/NBK100491/">the JATS to SPAR</a> work). This work continues to expand, as the list of <a href="/publications">new journal articles and conference papers about SPAR Ontologies</a> attests.</p>
<hr class="featurette-divider" />
<h3><a class="anchor" id="collabs"></a>
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2 changes: 1 addition & 1 deletion spar/ontology_descriptions/doco.txt
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Expand Up @@ -14,6 +14,6 @@

The creation of DoCO was undertaken by studying different corpora of documents (mainly scientific literature and web documents on different topics) and publishers' guidelines, from two perspectives – the structural and the rhetorical. In addition, some informal interviews have been done with researchers in different fields and with academic publishers, in order to gather as much information as possible about document components and their use.

DoCO imports the [Pattern Ontology](http://www.essepuntato.it/2008/12/pattern) that describes structural patterns (introduced in the paper entitled "[Dealing with structural patterns of XML documents](http://dx.doi.org/10.1002/asi.23088)"), and the [Discourse Element Ontology (DEO)](/ontologies/deo), which was developed with DoCO and describes rhetorical components. Additionally, it also defines hybrid classes describing elements that are both structural and rhetorical in nature, such as paragraph (``doco:Paragraph``), section (``doco:Section``) or list (``doco:List``). DoCO is also aligned with the [SALT Rhetorical Ontology](http://lov.okfn.org/dataset/lov/vocabs/sro) and the [Ontology of Rhetorical Blocks (ORB)](http://www.w3.org/2001/sw/hcls/notes/orb/). A concise summary of the main DoCO classes and its imported ontologies is shown in the following figure.
DoCO imports the [Pattern Ontology](http://www.essepuntato.it/2008/12/pattern) that describes structural patterns (introduced in the paper entitled "[Dealing with structural patterns of XML documents](https://doi.org/10.1002/asi.23088)"), and the [Discourse Element Ontology (DEO)](/ontologies/deo), which was developed with DoCO and describes rhetorical components. Additionally, it also defines hybrid classes describing elements that are both structural and rhetorical in nature, such as paragraph (``doco:Paragraph``), section (``doco:Section``) or list (``doco:List``). DoCO is also aligned with the [SALT Rhetorical Ontology](http://lov.okfn.org/dataset/lov/vocabs/sro) and the [Ontology of Rhetorical Blocks (ORB)](http://www.w3.org/2001/sw/hcls/notes/orb/). A concise summary of the main DoCO classes and its imported ontologies is shown in the following figure.

<img class="img-responsive center-block" src="/static/img/spar/doco-architecture.png" alt="A summary of the main classes defined in DoCO and its related imported ontologies." />
6 changes: 3 additions & 3 deletions spar/ontology_examples/bido.txt
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Expand Up @@ -32,7 +32,7 @@ journal:journal-of-web-semantics a fabio:Journal ;
:thomson-reuters a foaf:Organization ;
foaf:homepace <http://thomsonreuters.com> .

#cite Peroni, Silvio (2015): Example of use of BiDO #1. figshare. http://dx.doi.org/10.6084/m9.figshare.1559974
#cite Peroni, Silvio (2015): Example of use of BiDO #1. figshare. https://doi.org/10.6084/m9.figshare.1559974


#id bido_2
Expand Down Expand Up @@ -87,7 +87,7 @@ For instance, in the example we assign a particular research category (defined m
bido:hasStrength bido:low ;
bido:hasGrowth bido:logarithmic .

#cite Peroni, Silvio (2015): Example of use of BiDO #2. figshare. http://dx.doi.org/10.6084/m9.figshare.1559973
#cite Peroni, Silvio (2015): Example of use of BiDO #2. figshare. https://doi.org/10.6084/m9.figshare.1559973


#id bido_3
Expand Down Expand Up @@ -146,4 +146,4 @@ conf:cade1980-cff-rank a bido:BibliometricDataInTime ;
"Computing Research and Education Association of Australasia" ;
foaf:homepage <http://www.core.edu.au> .

#cite Peroni, Silvio (2015): Example of use of BiDO #3. figshare. http://dx.doi.org/10.6084/m9.figshare.1559979
#cite Peroni, Silvio (2015): Example of use of BiDO #3. figshare. https://doi.org/10.6084/m9.figshare.1559979
16 changes: 8 additions & 8 deletions spar/ontology_examples/biro.txt
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#title Defining bibliographic references and reference lists

#description The paper entitled "[Intertextual semantics: A semantics for information design](http://dx.doi.org/10.1002/asi.21134)" contains a list of references, each of them referring to a particular published article. For instance, the content of a particular bibliographic reference contained in that list, and referring to the paper "[Towards a semantics for XML markup](http://dx.doi.org/10.1145/585058.585081)", is:
#description The paper entitled "[Intertextual semantics: A semantics for information design](https://doi.org/10.1002/asi.21134)" contains a list of references, each of them referring to a particular published article. For instance, the content of a particular bibliographic reference contained in that list, and referring to the paper "[Towards a semantics for XML markup](http://dx.doi.org/10.1145/585058.585081)", is:

> Renear, A., Dubin, D. & Sperberg-McQueen, C.M. (2002). Towards a semantics for XML markup. In E. Mudson (Chair), Proceedings of the ACM Symposium on Document Engineering, (pp. 119-126). New York: ACM Press.

Expand All @@ -14,7 +14,7 @@ A first necessary step to release bibliographic references like the above one in
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix frbr: <http://purl.org/vocab/frbr/core#> .

<http://dx.doi.org/10.1002/asi.21134>
<https://doi.org/10.1002/asi.21134>
frbr:part :reference-list .

:reference-list a biro:ReferenceList ;
Expand Down Expand Up @@ -54,9 +54,9 @@ A first necessary step to release bibliographic references like the above one in
In E. Mudson (Chair), Proceedings of the ACM
Symposium on Document Engineering, (pp. 119-126).
New York: ACM Press." ;
biro:references <http://dx.doi.org/10.1145/585058.585081> .
biro:references <https://doi.org/10.1145/585058.585081> .

#cite Peroni, Silvio (2015): Example of use of BiRO #1. figshare. http://dx.doi.org/10.6084/m9.figshare.1534592
#cite Peroni, Silvio (2015): Example of use of BiRO #1. figshare. https://doi.org/10.6084/m9.figshare.1534592


#id biro_2
Expand Down Expand Up @@ -110,7 +110,7 @@ This pattern allows one to describe each string of a bibliographic reference as
foaf:givenName "Allen" ;
foaf:familyName "Renear" .

#cite Peroni, Silvio (2015): Example of use of BiRO #2. figshare. http://dx.doi.org/10.6084/m9.figshare.1534651
#cite Peroni, Silvio (2015): Example of use of BiRO #2. figshare. https://doi.org/10.6084/m9.figshare.1534651


#id biro_3
Expand All @@ -119,13 +119,13 @@ This pattern allows one to describe each string of a bibliographic reference as

#description Another approach, alternative to the one presented in the [second BiRO example](#biro_2), to deal with the semantic enhancement of bibliographic references is to use [EARMARK](http://www.essepuntato.it/2008/12/earmark) ranges for associating appropriate semantic statements to textual fragments, as illustrated in the following paper:

<p class="cite bg-info">Peroni, S., Gangemi, A., & Vitali, F. (2011). Dealing with markup semantics. In Proceedings the 7th International Conference on Semantic Systems (i-Semantics 2011): 111–118. http://dx.doi.org/10.1145/2063518.2063533</p>
<p class="cite bg-info">Peroni, S., Gangemi, A., & Vitali, F. (2011). Dealing with markup semantics. In Proceedings the 7th International Conference on Semantic Systems (i-Semantics 2011): 111–118. https://doi.org/10.1145/2063518.2063533</p>

For instance, the reference introduced in the [first BiRO example](#biro_1) can be encoded as an EARMARK document. We first need a particular string container called docuverse in EARMARK (corresponding to the class ``earmark:StringDocuverse``). This entity allows one to define the text of the reference. Then, we can define ranges (the class ``earmark:PointerRange``) for each string we want to use in order to describe the bibliographic reference according to [BiRO](/ontologies/biro).

Furthermore, using the [LA-EARMARK](http://www.essepuntato.it/2013/06/la-earmark), and extension of EARMARK for expressing markup semantics, it is possible to link EARMARK ranges to their formal meaning and to the particular object referenced by such strings, as described in the following work:

<p class="cite bg-info">Barabucci, G., Di Iorio, A., Peroni, S., Poggi, F., & Vitali, F. (2013). Annotations with EARMARK in practice: a fairy tale. In Proceedings of DH-CASE 2013. http://dx.doi.org/10.1145/2517978.2517990</p>
<p class="cite bg-info">Barabucci, G., Di Iorio, A., Peroni, S., Poggi, F., & Vitali, F. (2013). Annotations with EARMARK in practice: a fairy tale. In Proceedings of DH-CASE 2013. https://doi.org/10.1145/2517978.2517990</p>

We can say that a certain range (i.e., a string) actually denotes (``la:denotes``) a particular concrete object, i.e., a particular person identified by a certain IRI. Specifically, that range expresses (``la:expresses``) a particular meaning (``la:Meaning``), i.e., the fact that the string (as well as the denoted object) refers to something being an author of that paper.

Expand Down Expand Up @@ -203,4 +203,4 @@ We can say that a certain range (i.e., a string) actually denotes (``la:denotes`
foaf:givenName "Allen" ;
foaf:familyName "Renear" .

#cite Peroni, Silvio (2015): Example of use of BiRO #3. figshare. http://dx.doi.org/10.6084/m9.figshare.1535530
#cite Peroni, Silvio (2015): Example of use of BiRO #3. figshare. https://doi.org/10.6084/m9.figshare.1535530
20 changes: 10 additions & 10 deletions spar/ontology_examples/c4o.txt
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#title Describing citation contexts

#description In a particular sentence of the paper entitled "[Intertextual semantics: A semantics for information design](http://dx.doi.org/10.1002/asi.21134)" there is a citation to the paper "[Towards a semantics for XML markup](http://dx.doi.org/10.1145/585058.585081)" made through a in-text reference pointer to a specific bibliographic reference.
#description In a particular sentence of the paper entitled "[Intertextual semantics: A semantics for information design](https://doi.org/10.1002/asi.21134)" there is a citation to the paper "[Towards a semantics for XML markup](http://dx.doi.org/10.1145/585058.585081)" made through a in-text reference pointer to a specific bibliographic reference.

[C4O](/ontologies/c4o) enables ontological descriptions of the citation context where an in-text reference pointer appears in the citing document, and allows one to relate that context to relevant textual passages in the cited document.

Expand All @@ -13,7 +13,7 @@
@prefix doco: <http://purl.org/spar/doco/> .
@prefix frbr: <http://purl.org/vocab/frbr/core#> .

<http://dx.doi.org/10.1002/asi.21134>
<https://doi.org/10.1002/asi.21134>
frbr:part :in-text-renear02 , :renear02 .

:in-text-renear02 a c4o:InTextReferencePointer ;
Expand All @@ -26,14 +26,14 @@
Towards a semantics for XML markup. In E. Mudson (Chair),
Proceedings of the ACM Symposium on Document Engineering,
(pp. 119-126). New York: ACM Press." ;
biro:references <http://dx.doi.org/10.1145/585058.585081> .
biro:references <https://doi.org/10.1145/585058.585081> .

:citation-sentence a doco:Sentence ;
c4o:hasContent
"Renear, Dubin, and Sperberg-McQueen (2002, pp. 121-122)
proposed a formal semantic approach for structured documents." .

<http://dx.doi.org/10.1145/585058.585081>
<https://doi.org/10.1145/585058.585081>
frbr:part :cited-sentence .

:cited-sentence a doco:Sentence ;
Expand All @@ -43,7 +43,7 @@
those structures, relationships, and properties explicit." ;
c4o:isRelevantTo :citation-sentence .

#cite Peroni, Silvio (2015): Example of use of C4O #1. figshare. http://dx.doi.org/10.6084/m9.figshare.1536253
#cite Peroni, Silvio (2015): Example of use of C4O #1. figshare. https://doi.org/10.6084/m9.figshare.1536253


#id c4o_2
Expand All @@ -52,7 +52,7 @@

#description [C4O](/ontologies/c4o) allows one to record the number of citations a cited entity has received globally (property ``c4o:hasGlobalCitationCount``), as determined by a bibliographic information resource (property ``c4o:hasGlobalCountSource``) such as [Google Scholar](http://scholar.google.com), [Scopus](http://www.scopus.com) or [Web of Knowledge](http://apps.isiknowledge.com) on a particular date (property ``c4o:hasGlobalCountDate``).

For instance we can write a set of assertions according to C4O that describe how many times the reference - contained in the paper "[Intertextual semantics: A semantics for information design](http://dx.doi.org/10.1002/asi.21134)" and referring to the paper "[Towards a semantics for XML markup](http://dx.doi.org/10.1145/585058.585081)" - is used within the citing article and how much the cited article is globally cited according to Google Scholar.
For instance we can write a set of assertions according to C4O that describe how many times the reference - contained in the paper "[Intertextual semantics: A semantics for information design](https://doi.org/10.1002/asi.21134)" and referring to the paper "[Towards a semantics for XML markup](http://dx.doi.org/10.1145/585058.585081)" - is used within the citing article and how much the cited article is globally cited according to Google Scholar.

#code @prefix : <http://www.sparontologies.net/example/> .
@prefix biro: <http://purl.org/spar/biro/> .
Expand All @@ -63,7 +63,7 @@ For instance we can write a set of assertions according to C4O that describe how
@prefix frbr: <http://purl.org/vocab/frbr/core#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<http://dx.doi.org/10.1002/asi.21134>
<https://doi.org/10.1002/asi.21134>
frbr:part :renear02 .

:renear02 a biro:BibliographicReference ;
Expand All @@ -72,10 +72,10 @@ For instance we can write a set of assertions according to C4O that describe how
Towards a semantics for XML markup. In E. Mudson (Chair),
Proceedings of the ACM Symposium on Document Engineering,
(pp. 119-126). New York: ACM Press." ;
biro:references <http://dx.doi.org/10.1145/585058.585081> ;
biro:references <https://doi.org/10.1145/585058.585081> ;
c4o:hasInTextCitationFrequency "1"^^xsd:nonNegativeInteger .

<http://dx.doi.org/10.1145/585058.585081>
<https://doi.org/10.1145/585058.585081>
c4o:hasGlobalCitationFrequency :g-citation-2014-03-17 .

:g-citation-2014-03-17 a c4o:GlobalCitationCount ;
Expand All @@ -86,4 +86,4 @@ For instance we can write a set of assertions according to C4O that describe how
:google-scholar a c4o:BibliographicInformationSource ;
foaf:homepage <http://scholar.google.com> .

#cite Peroni, Silvio (2015): Example of use of C4O #2. figshare. http://dx.doi.org/10.6084/m9.figshare.1536254
#cite Peroni, Silvio (2015): Example of use of C4O #2. figshare. https://doi.org/10.6084/m9.figshare.1536254
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