Automating Semantic Publishing
keyword: CISE
keyword: Curry-Howard Isomorphism
keyword: Genuine Semantic Publishing
keyword: Principle of Compositionality
keyword: Semantic Publishing
keyword: Structural Patterns
keyword: Structural Semantics
part: Abstract
part: Compositional and iterative semantic enhancement of scholarly articles
part: Conclusions
part: diiorio2013
part: diiorio2014
part: diiorio2014 2
part: Implementations of CISE
part: gangemi2017
part: Print, Digital, and Semantic Publishing
part: Limitations and future directions
part: odt2006
part: A pathway from syntax to semantics
part: references
part: Related works

main-argument-evidence1
type: Evidence
description: in a community (e.g., a conference or a journal) that specifies the use of a very extensive, permissive, and non-pattern-based markup language, the large majority of authors use a pattern-based subset of such language for writing their scholarly articles
proves: main-argument-claim
supports: main-argument-warrant

main-argument-evidence2
type: Evidence
description: only a small number of pattern-based documents, stored by using the same markup language and coming from different communities of authors, is needed for automatically generating generic visualisations for all documents stored in that markup language (regardless they are pattern-based or not) included in the communities in consideration
proves: main-argument-claim
supports: main-argument-warrant

main-argument-evidence3
type: Evidence
description: only a small number of pattern-based documents, written by different authors of the same community, is needed for extracting the structural semantics of the main components of all the documents included in that community. This conclusion has been derived by analysing the outcomes of the algorithm execution, as illustrated in .
proves: main-argument-claim
supports: main-argument-warrant

Abstract
type: Section
role: doc-abstract

campbell1974
type: BibliographicReference
references: 978-1-349-01892-5 11
has content: Donald T. Campbell (1974). Downward causation in hierarchically organised biological systems. In Francisco Jose Ayala and Theodosius Dobzhansky (Eds.), Studies in the philosophy of biology: 179-186. DOI: https://doi.org/10.1007/978-1-349-01892-5_11
role: doc-biblioentry

Compositional and iterative semantic enhancement of scholarly articles
type: Contribution
type: Section

comeau2013
type: BibliographicReference
references: bat064
has content: Donald C. Comeau, Rezarta Islamaj Doğan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifan Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur (2013). BioC: a minimalist approach to interoperability for biomedical text processing. Database, 2013: bat064. DOI: https://doi.org/10.1093/database/bat064
role: doc-biblioentry

Conclusions
type: Conclusion
type: Section

diiorio2013b
type: BibliographicReference
references: 978-3-642-41242-4 6
has content: Angelo Di Iorio, Andrea G. Nuzzolese, Silvio Peroni (2013). characterizing citations in scholarly documents: the CiTalO framework. In ESWC 2013 Satellite Events - Revised Selected Papers: 66-77. DOI: http://doi.org/10.1007/978-3-642-41242-4_6
role: doc-biblioentry

Implementations of CISE
type: Evaluation
type: Section
links to: deo
links to: doco
links to: earmark
links to: pattern
part: constantin2016-p1
part: constantin2016-p2
part: diiorio2011-p1
part: diiorio2014-p1
part: layer1-layer2
part: layer2-layer3
part: layer3-layer4

fink2010
type: BibliographicReference
references: https://doi.org/10.1186/1471-2105-11-103
has content: J. Lynn Fink, Pablo Fernicola, Rahul Chandran, Savas Parastatidis, Alex Wade, Oscar Naim, Gregory B. Quinn, Philip E. Bourne (2010). Word add-in for ontology recognition: semantic enrichment of scientific literature. BMC Bioinformatics, 2010 (11): 103 DOI: https://doi.org/10.1186/1471-2105-11-103
role: doc-biblioentry

gangemi2013
type: BibliographicReference
references: 978-3-642-38288-8 24
has content: Aldo Gangemi (2013). A Comparison of Knowledge Extraction Tools for the Semantic Web. In Proceedings of the 10th Extended Semantic Web Conference (ESWC 2013): 351-366. DOI: https://doi.org/10.1007/978-3-642-38288-8_24
role: doc-biblioentry

Print, Digital, and Semantic Publishing
type: Introduction
type: Section
links to: rstl.royalsocietypublishing.org
links to: fred
links to: www.thelancet.com
links to: ARPANET
links to: Downward causation
links to: Electronic publishing
links to: Internet
links to: Johannes Gutenberg
links to: Philosophical Transactions of the Royal Society
links to: Principle of compositionality
links to: Royal Society
links to: The Lancet
links to: World Wide Web
links to: rash
links to: spar-xtractor
part: bagnacani2014-p1
part: bernerslee2001-p1
part: cyganiak2014-p1
part: gangemi2017-p1
part: groth2010-p1
part: pelletier1994-p1
part: peroni2016-p1
part: peroni2016-p2
part: shotton2009-p1
part: shotton2009 2-p1
part: wilkinson2016-p1

jha2017
type: BibliographicReference
references: S1351324915000443
has content: Rahul Jha, Amjad-Abu Jbara, Vahed Qazvinian, Dragomir R. Radev (2017). NLP-driven citation analysis for scientometrics. Natural Language Engineering, 23 (1): 93-130. DOI: https://doi.org/10.1017/S1351324915000443
role: doc-biblioentry

kim2000
type: BibliographicReference
references: https://doi.org/10.1117/12.410828
has content: Jongwoo Kim, Daniel X. Le, George R. Thoma (2000). Automated Labeling in Document Images. In Proceedings of Document Recognition and Retrieval VIII: 111-122. DOI: https://doi.org/10.1117/12.410828
role: doc-biblioentry

koh2007
type: BibliographicReference
references: https://doi.org/10.1145/1284420.1284466
has content: Eunyee Koh, Daniel Caruso, Andruid Kerne, Ricardo Gutierrez-Osuna (2007). Elimination of junk document surrogate candidates through pattern recognition. In Proceedings of the 2007 ACM symposium on Document engineering (DocEng07): 187-195. DOI: https://doi.org/10.1145/1284420.1284466
role: doc-biblioentry

liakata2010
type: BibliographicReference
references: 644 Paper.pdf
has content: Maria Liakata, Simone Teufel, Advaith Siddharthan, Colin Batchelor (2010). In Proceedings of the 7th International Conference on Language Resources and Evaluation (LREC 2010): 2054-2061. http://www.lrec-conf.org/proceedings/lrec2010/pdf/644_Paper.pdf
role: doc-biblioentry

Limitations and future directions
type: Discussion
type: Section
links to: ontology
links to: cito
links to: fabio
links to: argumentmodel
part: lehmann2015-p1
part: peroni2012-p1
part: peroni2012-p2

livingston2013
type: BibliographicReference
references: https://doi.org/10.1186/2041-1480-4-38
has content: Kevin M. Livingston, Michael Bada, Lawrence E. Hunter, Karin Verspoor (2013). Representing annotation compositionality and provenance for the Semantic Web. Journal of Biomedical Semantics, 2013 (4): 38. DOI: https://doi.org/10.1186/2041-1480-4-38
role: doc-biblioentry

moreau2013
type: BibliographicReference
references: prov-dm
has content: Luc Moreau, Paolo Missier (2013). PROV-DM: The PROV Data Model. W3C Recommendation 30 April 2013. http://www.w3.org/TR/prov-dm/
role: doc-biblioentry

noble2008
type: BibliographicReference
references: the-music-of-life-9780199228362
has content: Denis Noble (2008). The Music of Life: Biology beyond genes. Oxford University Press. ISBN: 9780199228362. https://global.oup.com/academic/product/the-music-of-life-9780199228362
role: doc-biblioentry

A pathway from syntax to semantics
type: RelatedWork
type: Section
part: crick1966-p1
part: fox2010-p1
part: howard1980-p1
part: montague1970-p1
part: pelletier1994-p2
part: sperbergmcqueen2004-p1
part: toulmin1958-p1

Related works
type: RelatedWork
type: Section

sanderson2017
type: BibliographicReference
references: annotation-model
has content: Robert Sanderson, Paolo Ciccarese, Benjamin Young (2017). Web Annotation Data Model. W3C Recommendation 23 February 2017. https://www.w3.org/TR/annotation-model/
role: doc-biblioentry

sateli2015
type: BibliographicReference
references: peerj-cs.37
has content: Bahar Sateli​, René Witte (2015).​ Semantic representation of scientific literature: bringing claims, contributions and named entities onto the Linked Open Data cloud. PeerJ Computer Science: e37. DOI: https://doi.org/10.7717/peerj-cs.37
role: doc-biblioentry

taghva2006
type: BibliographicReference
references: https://doi.org/10.1007/BFb0053288
has content: Kazem Taghva, Allen Condit, Julie Borsack (2006). Autotag: a tool for creating structured document collections from printed materials. In Proceedings of the 7th International Conference on Electronic Publishing (EP 2007): 420-431. DOI: https://doi.org/10.1007/BFb0053288
role: doc-biblioentry

tannier2005
type: BibliographicReference
references: https://doi.org/10.1145/1096601.1096638
has content: Xavier Tannier, Jean-Jacques Girardot, Mihaela Mathieu (2005). Classifying XML tags through “reading contexts”. In Proceedings of the 2005 ACM symposium on Document engineering (DocEng05): 143-145. DOI: https://doi.org/10.1145/1096601.1096638
role: doc-biblioentry

teufel2006
type: BibliographicReference
references: https://doi.org/10.3115/1610075.1610091
has content: Simone Teufel, Advaith Siddharthan, Dan Tidhar (2006). Automatic classification of citation function. In Proceedings of the 2006 Conference on Empirical Methods in Natural Language Processing (EMNLP 2006): 103-110. DOI: https://doi.org/10.3115/1610075.1610091
role: doc-biblioentry

zou2007
type: BibliographicReference
references: https://doi.org/10.1145/1284420.1284468
has content: Jie Zou, Daniel Le, George R. Thoma (2007). Structure and Content Analysis for HTML Medical Articles: A Hidden Markov Model Approach. In Proceedings of the 2007 ACM symposium on Document engineering (DocEng07): 199-201. DOI: https://doi.org/10.1145/1284420.1284468
role: doc-biblioentry

Silvio Peroni
type: Person
has ORCID: 0000-0003-0530-4305
holds role in time: affiliation
holds role in time: author
affiliation: Digital And Semantic Publishing Laboratory, Department of Computer Science and Engineering, University of Bologna, Bologna, Italy

bagnacani2014
type: BibliographicReference
references: 978-3-319-17966-7 10
has content: Andrea Bagnacani, Paolo Ciancarini, Angelo Di Iorio, Andrea Giovanni Nuzzolese, Silvio Peroni, Fabio Vitali (2014). The Semantic Lancet Project: A Linked Open Dataset for Scholarly Publishing. In EKAW (Satellite Events) 2014: 101-105. DOI: https://doi.org/10.1007/978-3-319-17966-7_10
role: doc-biblioentry

bernerslee2001
type: BibliographicReference
references: scientificamerican0501-34
has content: Tim Berners-Lee, James Hendler, Ora Lassila (2001). The Semantic Web. Scientific American, 285 (5): 34-43. DOI: https://doi.org/10.1038/scientificamerican0501-34
role: doc-biblioentry

crick1966
type: BibliographicReference
references: CRIOMA
has content: Francis Crick (1966). Of Molecules and Men. University of Washington Press. ISBN: 1591021855. https://philpapers.org/rec/CRIOMA
role: doc-biblioentry

cyganiak2014
type: BibliographicReference
references: rdf11-concepts
has content: Richard Cyganiak, David Wood, Markus Lanthaler (2014). RDF 1.1 Concepts and Abstract Syntax. W3C Recommendation 25 February 2014. https://www.w3.org/TR/rdf11-concepts/
role: doc-biblioentry

diiorio2014 2
type: BibliographicReference
references: lisc2014 submission 6.pdf
has content: Angelo Di Iorio, Silvio Peroni, Fabio Vitali, Jacopo Zingoni (2014). Semantic Lenses to Bring Digital and Semantic Publishing Together. In Proceedings of the 4th Workshop on Linked Science 2014 (LISC2014): 12-23. http://ceur-ws.org/Vol-1282/lisc2014_submission_6.pdf
role: doc-biblioentry

fox2010
type: BibliographicReference
references: jcb.201004062
has content: Rebecca M. Fox, Caitlin D. Hanlon, and Deborah J. Andrew (2010). The CrebA/Creb3-like transcription factors are major and direct regulators of secretory capacity. Journal of Cell Biology, 191 (3): 479-492. DOI: https://doi.org/10.1083/jcb.201004062
role: doc-biblioentry

groth2010
type: BibliographicReference
references: ISU-2010-0613
has content: Paul Groth, Andrew Gibson, Jan Velterop (2010). The anatomy of a nanopublication. Information Services and Use, 30 (1-2): 51-56. DOI: https://doi.org/10.3233/ISU-2010-0613
role: doc-biblioentry

howard1980
type: BibliographicReference
references: howard.pdf
has content: William A. Howard (1980). The formulae-as-types notion of construction. In Jonathan P. Seldin, J. Roger Hindley, To H.B. Curry: Essays on Combinatory Logic, Lambda Calculus and Formalism: 479-490. Boston, MA: Academic Press. ISBN: 978-0-12-349050-6. http://www.dcc.fc.up.pt/~acm/howard.pdf (last visited May 30, 2017)
role: doc-biblioentry

lehmann2015
type: BibliographicReference
references: SW-140134
has content: Jens Lehmann, Robert Isele, Max Jakob, Anja Jentzsch, Dimitris Kontokostas, Pablo N. Mendes, Sebastian Hellmann, Mohamed Morsey, Patrick van Kleef, Sören Auer, Christian Bizer (2015). DBpedia - A large-scale, multilingual knowledge base extracted from Wikipedia. Semantic Web, 6 (2): 167-195. DOI: https://doi.org/10.3233/SW-140134
role: doc-biblioentry

montague1970
type: BibliographicReference
references: j.1755-2567.1970.tb00434.x
has content: Richard Montague (1970). Universal grammar. Theoria, 36 (3): 373-398. DOI: https://doi.org/10.1111/j.1755-2567.1970.tb00434.x
role: doc-biblioentry

odt2006
type: BibliographicReference
references: http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm
has content: JTC1/SC34 WG 6. (2006). ISO/IEC 26300:2006 - Information technology - Open Document Format for Office Applications (OpenDocument) v1.0. Geneva, Switzerland: International Organization for Standardization. http://www.iso.org/iso/iso_catalogue/catalogue_tc/catalogue_detail.htm?csnumber=43485
role: doc-biblioentry

shotton2009
type: BibliographicReference
references: https://doi.org/10.1087/2009202
has content: David Shotton (2009). Semantic publishing: the coming revolution in scientific journal publishing. Learned Publishing, 22 (2): 85-94. DOI: https://doi.org/10.1087/2009202
role: doc-biblioentry

shotton2009 2
type: BibliographicReference
references: journal.pcbi.1000361
has content: David Shotton, Katie Portwin, Graham Klyne, Alistair Miles (2009). Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Computational Biology, 5 (4). DOI: https://doi.org/10.1371/journal.pcbi.1000361
role: doc-biblioentry

sperbergmcqueen2004
type: BibliographicReference
references: 978-3-540-39916-2 12
has content: Michael Sperberg-McQueen, Claus Huitfeldt (2004). GODDAG: A Data Structure for Overlapping Hierarchies. In Proceedings of the 5th International Workshop on Principles of Digital Document Processing (PODDP 2000): 139-160. DOI: https://doi.org/10.1007/978-3-540-39916-2_12
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teiconsortium2016
type: BibliographicReference
references: http://www.tei-c.org/release/doc/tei-p5-doc/en/html/
has content: Text Encoding Initiative Consortium (2016). TEI P5: Guidelines for Electronic Text Encoding and Interchange. http://www.tei-c.org/release/doc/tei-p5-doc/en/html/ (last visited May 30, 2017)
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toulmin1958
type: BibliographicReference
references: toulmin-the-uses-of-argument 1.pdf
has content: Stephen Toulmin (1958). The uses of argument. Cambridge, Cambridge University Press. ISBN: 9780521827485. http://johnnywalters.weebly.com/uploads/1/3/3/5/13358288/toulmin-the-uses-of-argument_1.pdf (last visited May 30, 2017)
role: doc-biblioentry

wilkinson2016
type: BibliographicReference
references: sdata.2016.18
has content: Mark D. Wilkinson, Michel Dumontier, IJsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E. Bourne, Jildau Bouwman, Anthony J. Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T. Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J.G. Gray, Paul Groth, Carole Goble, Jeffrey S. Grethe, Jaap Heringa, Peter A.C ’t Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J. Lusher, Maryann E. Martone, Albert Mons, Abel L. Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A. Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, Barend Mons (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data 3. DOI: https://doi.org/10.1038/sdata.2016.18
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constantin2016
type: BibliographicReference
references: SW-150177
has content: Alexandru Constantin, Silvio Peroni, Steve Pettifer, David M. Shotton, Fabio Vitali (2016). The Document Components Ontology (DoCO). Semantic Web, 7 (2): 167-181. DOI: https://doi.org/10.3233/SW-150177
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diiorio2011
type: BibliographicReference
references: asi.21591
has content: Angelo Di Iorio, Silvio Peroni, Fabio Vitali (2011). A Semantic Web approach to everyday overlapping markup. Journal of the American Society for Information Science and Technologies, 62 (9): 1696-1716: DOI: https://doi.org/10.1002/asi.21591
role: doc-biblioentry

diiorio2013
type: BibliographicReference
references: https://doi.org/10.1145/2494266.2494319
has content: Angelo Di Iorio, Silvio Peroni, Francesco Poggi, Fabio Vitali, David Shotton (2013). Recognising document components in XML-based academic articles. In Proceedings of the 2013 ACM Symposium on Document Engineering (DocEng 2013): 181-184. DOI: https://doi.org/10.1145/2494266.2494319
role: doc-biblioentry

gangemi2017
type: BibliographicReference
references: SW-160240
has content: Aldo Gangemi, Valentina Presutti, Diego Reforgiato Recupero, Andrea Giovanni Nuzzolese, Francesco Draicchio, Misael Mongiovì (2017). Semantic Web machine reading with FRED. Semantic Web, 8 (6). DOI: https://doi.org/10.3233/SW-160240
role: doc-biblioentry

pelletier1994
type: BibliographicReference
has content: Francis J. Pelletier (1994). The Principle of Semantic Compositionality. Topoi 13 (1): 11-24. DOI: https://doi.org/10.1007/BF00763644
role: doc-biblioentry

peroni2012
type: BibliographicReference
references: j.websem.2012.08.001
has content: Silvio Peroni, David Shotton (2012). FaBiO and CiTO: Ontologies for describing bibliographic resources and citations. Web Semantics, 17: 33-43. DOI: https://doi.org/10.1016/j.websem.2012.08.001
role: doc-biblioentry

peroni2016
type: BibliographicReference
references: peerj.preprints.2513
has content: Silvio Peroni, Francesco Osborne, Angelo Di Iorio, Andrea Giovanni Nuzzolese, Francesco Poggi, Fabio Vitali, Enrico Motta (2016). Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles. PeerJ PrePrints 4: e2513. DOI: https://doi.org/10.7287/peerj.preprints.2513
role: doc-biblioentry

walsh2010
type: BibliographicReference
references: docbook.html
has content: Norman Walsh (2010). DocBook 5: The Definitive Guide. Sebastopol, O'Reilly Media. ISBN: 9780596805029. http://tdg.docbook.org/tdg/5.0/docbook.html (last visited May 30, 2017)
role: doc-biblioentry

main-argument-claim
type: Claim
description: enable the implementation of mechanisms for the automatic enhancement of scholarly articles by considering the sole containment between their components

diiorio2014
type: BibliographicReference
references: asi.23088
has content: Angelo Di Iorio, Silvio Peroni, Francesco Poggi, Fabio Vitali (2014). Dealing with structural patterns of XML documents. Journal of the Association for Information Science and Technologies, 65 (9): 1884-1900. DOI: https://doi.org/10.1002/asi.23088
role: doc-biblioentry

main-argument-warrant
type: Warrant
description: outcomes of some experiments we have run by using these CISE-based algorithms are encouraging and they seem to suggest the applicability and feasibility of the whole approach
leads to: main-argument-claim