A semantic model for electronic publishing

Authors

  • Carlos Henrique Marcondes Universidade Federal Fluminense (UFF). Niterói, RJ, Brasil.

DOI:

https://doi.org/10.18617/liinc.v7i1.404

Keywords:

Electronic Publishing, Scientific Methodology, Scientific Communication, Knowledge Representation, Ontologies, Semantic Content Processing, E-Science

Abstract

Electronic publishing, although Information Technologies advancements, are still based in the print text model. The textual format prevents programs to semantic process articles content. A semantic model of scientific electronic publishing is proposed, in which conclusion are prompted by author and recorded in machine-understandable format, enabling semantic retrieval, identification of traces of scientific discoveries and knowledge misunderstandings. The model is based on concepts as deep, or semantic, structure of human language (CHOMSKY, 1975), of microstructure, macrostructure and superstructure (KINTSH & VAN DIJK, 1972), of rhetoric structure of scientific articles (HUTCHINS, 1977), (GROSS, 1990) and on scientific methodology semantic elements, such as problem, question, objective, hypothesis, experiment and conclusion. It results from analysis of 89 biomedical articles. A prototype system was developed which partially implements the model. Questionnaires with authors were used to test the prototype development. The prototype was also tested with several researchers-authors. Four patterns of reasoning and sequencing of semantic elements were identified in articles analyzed. The content model is implemented as a computational ontology. A prototype of a web author’s submission interface to a electronic journal system was developed and tested.

 

 

References

ALLSOPP, R. C.; VAZIRI, H.; PETTRSON, C.; GOLDSTEIN, S.;YOUGLAI, E. V.; FUTCHER, C. W.; GREIDER, C. W.; HARLEY, C. B. Telomere length predicts the replicative capacity of human fibroblasts, Proc. Nat. Acad. Sci. USA, v. 89, p. 10114-10118, 1992. The ArkeoteK Project. 2002. Disponível em: <http://www.arkeotek.org/>. Acesso em10 Jun. 2006.

BODENREIDER, O. Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support. In: IMIA Yearbook of Medical Informatics, :p. 67-79, 2008.

BUCKLAND, Michel. Information and Information Systems (Westport (CT). Praeger/Greenwood, 1991.

CARR, L.; MILES_BOARD, T.; WOUKEU, A.; WILL, G.; HALL, W. The case for explicit knowledge in documents. In: Proceedings of the 2004 ACM Symposium on Document Engineering, Milwaukee, Wisconsin, 2004 (ACM, 2004) 90-98. Disponível em : <http://www.eprints.ecs.soton.ac.uk/9360/>. Acesso em 6 maio 2006.

CHEN, J.; BLASCO, M. A.; GREIDER, C. W. Secondary structure of vertebrate telomerase RNA., Cell, v. 100, p. 503–514, 2000.

CHOMSKY, Noan. Aspectos da teoria da sintaxe. In: Textos selecionados. São Paulo: Abril Cultural, 1975. (Os Pensadores, 44).

COMMUNICATIONS IN PHYSICS. 2001. Disponível em: <http://www.science.uva.nl/projects/commmphys>. Acesso em 15 Mar. 2005.

COSTA, Leonardo Cruz da. Uma ferramenta para edição, extração e representação do conhecimento contido em artigos científicos publicados na web. Projeto de Tese de Doutorado para ingresso no PPGCI UFF/IBICT. Niterói, 2006.

COSTA, Leonardo Cruz da; MARCONDES, Carlos Henrique. Um ambiente para edição, extração e representação do conhecimento contido em artigos científicos publicados na web. In: ENANCIB - ENCONTRO NACIONAL DE PESQUISA EM CIÊNCIA DA INFORMAÇÃO,

São Paulo, set. 2008, 9, Anais... (Poster).

DAHLBERG, Ingetraut. Conceptual structures and systematization. International Forum on Information and Documentation, v. 20, n. 3, July, 1995. Data Documentation Initiative, 2004. Disponível em: . Acesso 29 fev. 2006.

DINAKARPADIAN, Deendayal; LEE, Yugyung; VISHWANATH, Kartik; LINGAMBHOTLA, ROHINI. MachineProse: An Ontological Framework for Scientific Assertions. Journal of the American Medical Informatics Association, v. 13, n. 2, Mar/Apr, p. 220-232, 2006. DOI 10.1197/jamia.M1910.

ELLIS, D. Paradigms and proto-paradigms in information retrieval research. In: P.Vakkari and B. Cronin (eds.), Conceptions of Library and Information Science: historical, empirical and theoretical perspectives. London: Graham Books, 1992. p. 165-186.

FRBR – FUNCTIONAL REQUIREMENTS FOR BIBLIOGRAPHIC RECORDS : final report / IFLA Study Group on the Functional Requirements for Bibliographic Records. München: K . G. Saur, 1998. (UBCIM Publications New Series).

GAO, Y; KINOSHITA, J.; WU, E.; MILLER, E.; LEE, R; SEABORNE, A.; CAYZER, S.; CLARK, T. SWAM: a distributed knowledge infrastructure for Alzeimer disease research, Journal of Web Semantic, v. 4, n. 3, 2006. Disponível em:

<http://www.websemanticsjournal.org/ps/pub/2006-17>. Acesso em 12 Dez.

GARDIN, J-C. Vers un remodelage des publications savantes: ses rapports avec sciences de l’information. In: Chaudrion & Fluhr (Eds). Filtrage et Résumé Automatique de l'Information sur les Reseaux - Actes du 3ème Colloque du Chapitre Français de l’ISKO, 2001.

GREIDER, C. W.; BLACKBURN, E. H. Identification of a specific telomere terminal transferase activity in Tetrahymena extracts, Cell, v. 43, p. 405-413, 1985.

GREIDER, C. W.; BLACKBURN, E. H. The telomere terminal transferase of Tetrahymena is a ribonucleoprotein enzyme with two kinds of primer specificity. Cell, v. 51, p. 887-898, 1987.

GROSS, A. G. The Rhetoric of Science. Cambridge, Massachusetts; London: Harvard University Press, 1990. ISBN 0-674-76873-6.

GUARINO, Nicola. Formal ontology, conceptual analysis and knowledge representation. International Journal of Human Computer Studies, v. 43, n. 5/6, p. 625-640, 1995.

GUIMARÃES, Carlos Alberto. Structured Abstracts. Narrative Review. Acta Cirúrgica Brasileira v. 21, n. 4, 2006. Disponível em < http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0102-86502006000400014 >. Acesso em 20 abril de 2009.

GUO-LIANG, Y.; BRADLEY, J. D.; ARTTARDI, L. D.; BLACKBURN, E. In vivo alteration of telomere sequences and senescence caused by mutated Tetrahymena telomerase RNAs. Nature, v. 344, p. 126-132, 1990.

HJORLAND, B. Epistemology and the sociocognitive perspective in information science, Journal of the American Society for Information Science and Technology, v. 53, n. 4, p. 257- 270, 2002.

HUCKA, M.; FINNEY, A.; BOLORI, H. System Biology Markup Language (SBML) Level 1: structures and facilities for basic model definitions (2003). Available at: http://www.sbml.org/specifications/sbml-level-1/version-2/sbml-level-1-v2.pdf (access 2 Nov. 2005).

HUNTER, L.; BAUMGARTNER Jr, A.; LU, Z.; JOHNSON, H. L.; CAPORASO, J. G.; PAQUETTE, J.; LINDERMANN, A.; WHITE, E. K.; MEDVEDEVA, O.; COHEN, K. B. Concept recognition for extracting protein interaction relations from biomedical text. Genome Biology, v. 9, 2008. Suppl. Disponível em <http://genomebiology.com/2008/9/S2/S9>. Acesso em 20 nov.20

HUTCHINS, J. On the structure of scientific texts. In: UEA Papers in Linguistics, Norwich. Norwich, UK: University of East Anglia, 1977, 5, Proceedings… p. 18-39. 1977. Disponível em <http://ourworld.compuserve.com/homepages/wjhutchins/UEAP/L-1977.pdf>. Acesso em 20 Mar 2006. International Committee of Medical Journals Editors. 2003. Retrieved 14 Jul. 2005 from at: www.icmje.org.

KANDO, N. Text-level structure of research papers: implications for text-based information processing systems. In: FURNER, J.; HARPER, D. J. (Eds.), Information Retrieval Research: Proceedings of the 19th BCS-IRSG Colloquium on IR Research, Aberdeen, 1997. Aberdeen, Scotland: Springer-Verlag, 1997.

KANDO, N. Text structure analysis as a tool to make retrieved documents usable. In: Proceedings of the 4th International Workshop on Information Retrieval with Asian Language, Taipei, 1999. Academia Sinica, Taipei, Taiwan, 1999.

KINTSH, W.; VAN DIJK, T. A. Towards a model of text comprehension and production, Psycological Review, v. 84, n. 5, p. 363-393, 1972.

KUHN, Thomas S. A estrutura das revoluções científicas. São Paulo: Perspectiva, 2003. (Série Debates Ciência).

FRAKLIN, Laura R. Exploratory Experiments. In Philosophy of Science Assoc. 19th Biennial Meeting - PSA2004: Contributed Papers, 2004, Proceedings…. Austin, Texas; 2004. Disponível em <http://philsci-archive.pitt.edu/archive/00002070/01/UploadedPSA2004.doc>. Acesso em 13 jun. 2008.

MAGNANI, L. Abduction, Reason, and Science: processes of discovery and explanation. New York: Kluwer Academic, Plenun Publishers, 2001.

MALHEIROS, Luciana Reis. A identificação de traços de descobertas científicas pela comparação do conteúdo de artigos em Ciências Biomédicas com uma ontologia pública. Tese (Doutorado em Ciência da Informação)-Programa de Pós-Graduação em Ciência da Informação convênio UFF/Ibict, Niterói, 2010.

MARCONDES, Carlos H. From scientific communication to public knowledge: the scientific article Web published as a knowledge base. In: Egelen, Jan, Dobreva, Milena, ed. ICCC ElPub - INTERNATIONAL CONFERENCE ON ELECTRONIC PUBLISHING, Leuven, Bélgica,

2005, 9, Proceedings... Leuven, Bélgica, 2005. p. 119-127. Disponível em <http://elpub.scix.net>.

MARCONDES, Carlos Henrique; MALHEIROS, Luciana Reis . Identifying traces scientific discoveries by comparing the content of articles in biomedical sciences with web ontologies. In: ISSI - International Conference on Informetrics and Scientometrics, 2009, Rio de Janeiro. 12, Proceedings. São Paulo: Bireme/PAHO/WHO, UFRJ, 2009. v. 1. p. 173-177.

MARCONDES, Carlos Henrique; MENDONÇA, Marília Alvarenga Rocha; MALHEIROS, Luciana Reis; COSTA, Leonardo Cruz da; SANTOS, Tatiana. Cristina Paredes. Bases ontológicas e conceituais para um modelo do conhecimento científico em artigos biomédicos. Reciis, v. 3, n. 1, p. 19-30, 2009. Disponível em <http://www.reciis.cict.fiocruz.br/index.php/reciis/article/view/240/251>. Acesso em 8 abr. 2009.

MCEACHERN, M. J.; BLACKBURN, E. H. Runaway telomere elongation cause by telomerase RNA mutations. Nature, n. 376, p. 403-409, 1995.

MURRAY-RUST, P.; RZEPA, H.S. STMML. A markup language for scientific, technical and medical publishing, Data Science Journal, v. 1, n. 2, p. 128-193, 2002. Available at: http://journals.eecs.qub.ac.uk/codata/journal/contents/1_2/1_2pdfs/ds121.pdf (accessed 18 Sept. 2005).

MURRAY-RUST, P.; RZEPA, H. S. Chemical Markup, XML and the worldwide web. I: basic principles, Journal of Chemical Information and Computer Science, v. 39, p. 928-942, 1999.

NILSSON, N.J. Principles of Artificial Intelligence. California: Tioga Publishing Co., 1980.

NWOGU, Kevin Ngozi. The Medical Research Paper: Structure and Functions. English for Specific Purposes, v. 16, n. 2, p. 119-138, 1997.

OBI – Ontology for Biomedical Investigations. 2008. Disponível em http://obi-ontology.org. Accesso 20 nov. 2008.

THE OPEN BIOLOGICAL AND BIOMEDICAL ONTOLOGIES. 2010. Disponível em <http://www.obofoundry.org/>. Acesso em 29 out. 2010.

OWL Ontology Web Language Overview. 2004. Disponível em: <http://www.w3.org/TR/owl- features/>. Acesso em 15 maio 2007.

RACUNAS, S. A.; SHAH, N. H.; I. ALBERT, I; FEDOROV, N. V. HyBrow: a prototype system for computer-aided hypothesis evaluation. Bioinformatics, v. 20, n.1, p. 257–264, 2004.

RDF Resource Description Framework. 2004. Disponível em: Retrieved January 7, 2007, from http://www.w3.org/RDF/. Acesso em 7 jan. 2007.

RDF Schema Specification. 2000. Disponível em: <http://www.w3.org/TR/2000/CR-rdf- schema-20000327/>. Acesso em 18 nov. 2010

RENEAR, Allen H.; PALMER, Carole. Strategic reading, ontologies and the future of scientific publishing. Science, v. 325, p. 828-832, 2009.

RESEARCH IN SEMANTIC SCHOLARLY PUBLISHING. 2005. Disponível em: htt://rssp.net/. Acesso em 13 Mar. 2006.

SCHOLARLY ONTOLOGIES PROJECT. 2004. Disponível em: <http://kmi.open.ac.uk/projects/scholarly>. Acesso em 12 Jun. 2005. Scientific Publishing Task Force – Ontology for Experiment Self-Publishing, 2006. Disponível em <http://esw.w3.org/topic/HCLS/SciPubSPERequirements>. Acesso em 15 Maio 2006.

SOLDATOVA, L. D; KING, R. D. An ontology of scientific experiments. Journal of the Royal Society Interface v. 3 n. 11, p. 795-803, 2006. Disponível em <http://journals.royalsociety.org/content/u552845783800t73/fulltext.pdf>. Acesso em 5 Fev 2008.

SHOTTON, David; PORTWIN, Katie; KLYNE, Graham; MILES, Alistair. Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article. PLoS Comput. Biol. v. 5, n. 4, April, 2009. Disponível em <http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2663789/>. Acesso em 27 jul. 2010.

SOWA, J. Knowledge Representation: logical, philosophical and computational foundations. Pacific Grove: Brooks/Cole, 2000.

SWALES, J. M. Genre analysis: english in academic and research settings. Nova Iorque: Cambridge University Press,1990.

TENOPIR, Carol; KING, Donald W. Electronic journals and changes in scholarly article seeking and reading patterns. Aslib Proceedings: New Information Perspectives, v. 61, n. 1, 2009. p. 5-32 Disponível em <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.156.2701&rep=rep1&type=pdf>. Acesso em 28 jun. 2010.

TEI: Text Encoding Initiative. 2005. Disponível em: http://www.tei-c.org. Acesso em 29 fev. 2006.

VICKERY, B.C. Knowledge representation: a brief review. Journal of Documentation, v. 42, n. 3, p. 145-59, 1986.

Published

01/04/2011

Issue

Section

XI Enancib: Information Science on Focus