CISE
Curry-Howard Isomorphism
Genuine Semantic Publishing
Principle of Compositionality
Semantic Publishing
Structural Patterns
Structural Semantics
Automating Semantic Publishing
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
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
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 .
Abstract
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
Compositional and iterative semantic enhancement of scholarly articles
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
Conclusions
Digital And Semantic Publishing Laboratory, Department of Computer Science and Engineering, University of Bologna, Bologna, Italy
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
Implementations of CISE
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
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
Print, Digital, and Semantic Publishing
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
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
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
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
Limitations and future directions
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
Luc Moreau, Paolo Missier (2013). PROV-DM: The PROV Data Model. W3C Recommendation 30 April 2013. http://www.w3.org/TR/prov-dm/
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
A pathway from syntax to semantics
Related works
Robert Sanderson, Paolo Ciccarese, Benjamin Young (2017). Web Annotation Data Model. W3C Recommendation 23 February 2017. https://www.w3.org/TR/annotation-model/
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
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
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
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
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
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
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
Francis Crick (1966). Of Molecules and Men. University of Washington Press. ISBN: 1591021855. https://philpapers.org/rec/CRIOMA
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/
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
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
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
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)
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
Richard Montague (1970). Universal grammar. Theoria, 36 (3): 373-398. DOI: https://doi.org/10.1111/j.1755-2567.1970.tb00434.x
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
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
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
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
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)
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)
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
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
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
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
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
Francis J. Pelletier (1994). The Principle of Semantic Compositionality. Topoi 13 (1): 11-24. DOI: https://doi.org/10.1007/BF00763644
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
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
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)
enable the implementation of mechanisms for the automatic enhancement of scholarly articles by considering the sole containment between their components
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
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