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Honorable Mention

Expressing High-Level Scientific Claims with Formal Semantics

Published:02 December 2021Publication History

ABSTRACT

The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the life sciences, computer science, and the social sciences. Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the "super-pattern''. We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door on the longer run for allowing researchers to express their high-level scientific findings in a manner they can be automatically interpreted. This in turn will allow for automated consistency checking, question answering, aggregation, and much more.

References

  1. Tim Berners-Lee and James A. Hendler. 2001. Publishing on the semantic web. Nature , Vol. 410 (2001), 1023--1024.Google ScholarGoogle ScholarCross RefCross Ref
  2. Arthur Brack et al. 2020 a. Domain-Independent Extraction of Scientific Concepts from Research Articles. In Advances in Information Retrieval . https://doi.org/10.1007/978--3-030--45439--5_17Google ScholarGoogle ScholarCross RefCross Ref
  3. Adrien Coulet et al. 2011a. Integration and publication of heterogeneous text-mined relationships on the Semantic Web. J Biomed Semant , Vol. 2 (2011). https://doi.org/10.1186/2041--1480--2-S2-S10Google ScholarGoogle ScholarCross RefCross Ref
  4. Alexandru Constantin et al. 2016. The Document Components Ontology (DoCO). Semantic Web , Vol. 7, 2 (February 2016), 167--181. https://doi.org/10.3233/SW-150177Google ScholarGoogle ScholarDigital LibraryDigital Library
  5. Angelo Di Iorio et al. 2014a. Semantic Lenses to Bring Digital and Semantic Publishing Together. In ISWC'14 , Vol. 128. 12--23.Google ScholarGoogle Scholar
  6. Aldo Gangemi et al. 2014b. The Publishing Workflow Ontology (PWO). Semantic Web , Vol. 8 (2014). https://doi.org/10.3233/SW-160230Google ScholarGoogle ScholarDigital LibraryDigital Library
  7. Cristina-Iulia Bucur et al. 2020 b. A Unified Nanopublication Model for Effective and User-Friendly Access to the Elements of Scientific Publishing. EKAW2020 (2020). https://doi.org/10.1007/978--3-030--61244--3_7Google ScholarGoogle ScholarCross RefCross Ref
  8. David Shotton et al. 2009. Adventures in semantic publishing: Exemplar semantic enhancements of a research article. PLoS computational biology , Vol. 5 (2009). Issue 4.Google ScholarGoogle Scholar
  9. Emek Demir et al. 2010a. The BioPAX community standard for pathway data sharing. Nat. Biotechnol. , Vol. 28 (2010). https://doi.org/10.1038/nbt.1666Google ScholarGoogle ScholarCross RefCross Ref
  10. Habeeb Ibrahim Abdul Razack et al. 2021. Artificial intelligence-assisted tools for redefining the communication landscape of the scholarly world. Science Editing , Vol. 8 (2021). https://doi.org/10.6087/kcse.244Google ScholarGoogle ScholarCross RefCross Ref
  11. Jaana Taakis et al. 2015a. Crowdsourced semantic annotation of scientific publications and tabular data in PDF. SEMANTICS'15 (2015).Google ScholarGoogle Scholar
  12. L. Garcia-Castro et al. 2013a. Connections across Scientific Publications based on Semantic Annotations. SEPublica (2013). https://doi.org/10.5167/UZH-82214Google ScholarGoogle ScholarCross RefCross Ref
  13. M.A. Angrosh et al. 2014c. Contextual information retrieval in research articles: Semantic publishing tools for the research community. Semantic Web , Vol. 5 (2014), 261--293. Issue 4. https://doi.org/0.5555/2786113.2786115Google ScholarGoogle ScholarDigital LibraryDigital Library
  14. Marcus C. Chibucos et al. 2014 d. Standardized description of scientific evidence using the Evidence Ontology (ECO). Database : the journal of biological databases and curation (2014). https://doi.org/10.1093/database/bau075Google ScholarGoogle ScholarCross RefCross Ref
  15. M. Hucka et al. 2003. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics , Vol. 19 (2003). https://doi.org/10.1093/bioinformatics/btg015Google ScholarGoogle ScholarCross RefCross Ref
  16. Mohamad Yaser Jaradeh et al. 2019 a. Open Research Knowledge Graph: Next Generation Infrastructure for Semantic Scholarly Knowledge. In KCAP'19 . https://doi.org/10.1145/3360901.3364435Google ScholarGoogle ScholarDigital LibraryDigital Library
  17. Paolo Ciccarese et al. 2011b. An open annotation ontology for science on web 3.0. J Biomed Semant , Vol. 2 (2011). https://doi.org/10.1186/2041--1480--2-S2-S4Google ScholarGoogle ScholarCross RefCross Ref
  18. Paolo Ciccarese et al. 2012a. Open semantic annotation of scientific publications using DOMEO. Journal of Biomedical Semantics , Vol. 3 (2012). https://doi.org/10.1186/2041--1480--3-S1-S1Google ScholarGoogle ScholarCross RefCross Ref
  19. Paul Groth et al. 2010b. The anatomy of a nanopublication. Information Services and Use , Vol. 30, 1--2 (2010). https://doi.org/10.3233/ISU-2010-0613Google ScholarGoogle ScholarCross RefCross Ref
  20. Pedro Sernadela et al. 2015b. A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results. WBBIO'2015 (2015). https://doi.org/10.1007/978--3--319--16483-0_2Google ScholarGoogle ScholarCross RefCross Ref
  21. Sören Auer et al. 2018. Towards a Knowledge Graph for Science. In WIMS'18 . https://doi.org/10.1145/3227609.3227689Google ScholarGoogle ScholarDigital LibraryDigital Library
  22. Sumit Madan et al. 2019 b. The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track. Database : the journal of biological databases and curation (2019). https://doi.org/10.1093/database/baz084Google ScholarGoogle ScholarCross RefCross Ref
  23. Silvio Peroni et al. 2012b. Scholarly publishing and Linked Data: describing roles, statuses, temporal and contextual extents. i-Semantics 2012 (2012). https://doi.org/10.1145/2362499.2362502Google ScholarGoogle ScholarDigital LibraryDigital Library
  24. Tobias Kuhn et al. 2013b. Broadening the scope of nanopublications. In Extended Semantic Web Conference . 487--5017. https://doi.org/10.1007/978--3--642--38288--8_33Google ScholarGoogle ScholarCross RefCross Ref
  25. Tobias Kuhn et al. 2013c. Broadening the Scope of Nanopublications (ESWC'13, Vol. 7882). ESWC: European Semantic Web Conference, Springer, 487--501. https://doi.org/10.1007/978--3--642--38288--8_33Google ScholarGoogle ScholarCross RefCross Ref
  26. Bryon Jacob and Jonathan Ortiz. 2017. Data.world: A Platform for Global-Scale Semantic Publishing. In ISWC'17 .Google ScholarGoogle Scholar
  27. Tobias Kuhn. 2018. Using the AIDA Language to Formally Organize Scientific Claims. CNL 2018 (2018). https://doi.org/10.3233/978--1--61499--904--1--52Google ScholarGoogle ScholarCross RefCross Ref
  28. Tobias Kuhn and Michel Dumontier. 2017. Genuine semantic publishing. Data Science , Vol. 1 (2017), 139--154. Issue 1/2. https://doi.org/10.3233/DS-170010Google ScholarGoogle ScholarCross RefCross Ref
  29. Esther Landhuis. 2016. Scientific literature: Information overload. Nature , Vol. 535 (2016), 457--458. https://doi.org/10.1038/nj7612--457aGoogle ScholarGoogle ScholarCross RefCross Ref
  30. Silvia Mirri et almbox. 2017. Towards accessible graphs in HTML-based scientific articles. In 4th IEEE Annual Consumer Communications & Networking Conference (CCNC) . 1067--1072. https://doi.org/10.1109/CCNC.2017.7983287Google ScholarGoogle ScholarDigital LibraryDigital Library
  31. Silvio Peroni. 2012. Semantic Publishing: issues, solutions and new trends in scholarly publishing within the Semantic Web era . PhD Thesis. Universita di Bologna. http://speroni.web.cs.unibo.it/publications/peroni-2012-semantic-publishing-issues.pdfGoogle ScholarGoogle Scholar
  32. Silvio Peroni. 2014. The Digital Publishing Revolution. In Semantic Web Technologies and Legal Scholarly Publishing, Pompeu Casanovas and Giovanni Sartor (Eds.). Law, Governance and Technology Series, Vol. 15. Springer International Publishing, Switzerland, Chapter 2, 7--43. https://doi.org/10.1007/978--3--319-04777--5_2Google ScholarGoogle ScholarCross RefCross Ref
  33. Silvio Peroni. 2017. Automating semantic publishing. Data Science , Vol. 1 (2017), 155--173. Issue 1/2. https://doi.org/10.3233/DS-170012Google ScholarGoogle ScholarCross RefCross Ref
  34. Silvio Peroni et almbox. 2017. Research Articles in Simplified HTML: a Web-first format for HTML-based scholarly articles. PeerJ Computer Science , Vol. 3 (2017). Issue e132. https://doi.org/10.7717/peerj-cs.132Google ScholarGoogle ScholarCross RefCross Ref
  35. Silvio Peroni and David Schotton. 2008. The SPAR Ontologies. ISWC 2018 Proceedings (2008). https://doi.org/10.1007/978--3-030-00668--6_8Google ScholarGoogle ScholarCross RefCross Ref
  36. Silvio Peroni and David Shotton. 2012. FaBiO and CiTO: ontologies for describing bibliographic resources and citations. Web Semantics: Science, Services and Agents on the World Wide Web , Vol. 17 (December 2012), 33--43. https://doi.org/10.1016/j.websem.2012.08.001Google ScholarGoogle ScholarCross RefCross Ref
  37. Peter Gordon Roetzel. 2019. Information overload in the information age: a review of the literature from business administration, business psychology, and related disciplines with a bibliometric approach and framework development. Business Research volume , Vol. 12 (2019). https://doi.org/10.1007/s40685-018-0069-zGoogle ScholarGoogle ScholarCross RefCross Ref
  38. Idafen Santana-Perez and María Poveda-Villalon. 2018. FAIR* Reviews Ontology (FR) . http://purl.org/spar/fr Retrieved September 14, 2021 fromGoogle ScholarGoogle Scholar
  39. Bahar Sateli and René Witte. 2016. From Papers to Triples: An Open Source Workflow for Semantic Publishing Experiments. In Semantics, Analytics, Visualization. Enhancing Scholarly Data . Springer, 39--44. https://doi.org/10.1007/978--3--319--53637--8_5Google ScholarGoogle ScholarCross RefCross Ref
  40. Pedro Sernadela and Jose Luis Oliveira. 2017. A semantic-based workflow for biomedical literature annotation. Database (Oxford) (2017). https://doi.org/10.1093/database/bax088Google ScholarGoogle ScholarCross RefCross Ref
  41. David Shotton. 2009. Semantic publishing: the coming revolution in scientific journal publishing. Learn. Publ. , Vol. 22 (2009), 85--94. Issue 2. https://doi.org/10.1087/2009202Google ScholarGoogle ScholarCross RefCross Ref
  42. Leslie F. Sikos. 2017. Knowledge Representation with Semantic Web Standards .Springer International Publishing, Cham, 11--49. https://doi.org/10.1007/978--3--319--54066--5_2Google ScholarGoogle ScholarCross RefCross Ref
  43. Ted Slater. 2014. Recent advances in modeling languages for pathway maps and computable biological networks. Drug Discovery Today , Vol. 19 (2014). https://doi.org/10.1016/j.drudis.2013.12.011Google ScholarGoogle ScholarCross RefCross Ref
  44. Ted Slater and Diane H. Song. 2012. Saved by the BEL: ringing in a common language for the life sciences. Fall (2012).Google ScholarGoogle Scholar
  45. Bodo M. Stern and Erin K. O'Shea. 2019. A proposal for the future of scientific publishing in the life sciences. PLoS Biol , Vol. 17, 2 (2019), 683--684. https://doi.org/10.1371/journal.pbio.3000116Google ScholarGoogle ScholarCross RefCross Ref

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    • Published in

      cover image ACM Conferences
      K-CAP '21: Proceedings of the 11th Knowledge Capture Conference
      December 2021
      300 pages
      ISBN:9781450384575
      DOI:10.1145/3460210

      Copyright © 2021 Owner/Author

      This work is licensed under a Creative Commons Attribution International 4.0 License.

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      Association for Computing Machinery

      New York, NY, United States

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      • Published: 2 December 2021

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