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Publishing DisGeNET as nanopublications

Queralt-Rosinach, Núria, Kuhn, Tobias, Chichester, Christine, Dumontier, Michel, Sanz, Ferran, Furlong, Laura I.·2016·Semantic Web
DOI 10.3233/sw-150189

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  • The nanopublication model has been used to represent statements from different fields, especially in the life science domain.

    “The nanopublication model has been used to represent statements from different fields, especially in the life science domain.”

    From Provenance-driven nanopublications: representing source lineage and trust networks for multi-source assertions (2025) · cites this paper as [7]

    The Abstract and Introduction (page not provided) describe nanopublications as a model for scientific statements and document their use for DisGeNET’s biomedical gene–disease associations. The Applications section also mentions nanopublications for other life-science datasets. Our copy does not establish that the model had been used to represent statements across different fields beyond life sciences. (LLM, conf=0.83)

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Research works printed but not linked: 18

  1. Bauer-Mehren, 2010, DisGeNET: A Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks, Bioinformatics, 26, 2924, 10.1093/bioinformatics/btq538 · DOI
  2. Beck, 2012, Semantically enabling a genome-wide association study database, Journal of Biomedical Semantics, 3, 9, 10.1186/2041-1480-3-9 · DOI
  3. K. Belhajjame, O. Corcho, D. Garijo, J. Zhao, P. Missier, D. Newman, R. Palma, S. Bechhofer, E. Garca Cuesta, J.M. Gomez-Perez, G. Klyne, K. Page, M. Roos, J.E. Ruiz, S. Soiland-Reyes, L. Verdes-Montenegro, D. De Roure and C. Goble, Workflow-centric research objects: First class citizens in scholarly discourse, in: SePublica 2012 Semantic Publishing, Proc. of the 2nd Workshop on Semantic Publishing, Hernissos, Crete, Greece, May 28th, 2012, A. García Castro, C. Lange, F. van Harmelen and B. Good, eds, CEUR Workshop Proceedings, Vol. 903, 2012, pp. 1–12.
  4. Bravo, 2015, Extraction of relations between genes and diseases from text and large-scale data analysis: Implications for translational research, BMC Bioinformatics, 16, 55, 10.1186/s12859-015-0472-9 · DOI
  5. A. Callahan, J. Cruz-Toledo, P. Ansell and M. Dumontier, Bio2RDF Release 2: Improved coverage, interoperability and provenance of Life Science Linked Data, in: The Semantic Web: Semantics and Big Data, Proc. of 10th International Conference, ESWC 2013, Montpeiller, France, May 26–30, 2013, P. Cimiano, O. Corcho, V. Presutti, L. Hollink and S. Rudolph, eds, Lecture Notes in Computer Science, Vol. 7882, Springer, Berlin, Heidelberg, 2013, pp. 200–212. · DOI
  6. Chichester, 2014, Querying neXtProt nanopublications and their value for insights on sequence variants and tissue expression, Journal of Web Semantics, 29, 15, 10.1016/j.websem.2014.05.001 · DOI · Paper page
  7. Ciccarese, 2013, PAV ontology: Provenance, authoring and versioning, Journal of Biomedical Semantics, 4, 37, 10.1186/2041-1480-4-37 · DOI
  8. Dumontier, 2014, The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery, Journal of Biomedical Semantics, 5, 14, 10.1186/2041-1480-5-14 · DOI
  9. Good, 2012, The Gene Wiki in 2011: Community intelligence applied to human gene annotation, Nucleic Acids Research, 40, D1255, 10.1093/nar/gkr925 · DOI
  10. Gray, 2014, Applying Linked Data approaches to pharmacology: Architectural decisions and implementation, Semantic Web Journal, 5, 101, 10.3233/SW-2012-0088 · DOI
  11. T. Kuhn and M. Dumontier, Trusty URIs: Verifiable, immutable, and permanent digital artifacts for Linked Data, in: The Semantic Web: Trends and Challenges, Proc. of 11th International Conference, ESWC 2014, Anissaras, Crete, Greece, May 25–29, 2014, V. Presutti, C. d’Amato, F. Gandon, M. d’Aquin, S. Staab and A. Tordai, eds, Lecture Notes in Computer Science, Vol. 8465, Springer International Publishing, Switzerland, 2014, pp. 395–410. · DOI
  12. J.P. McCusker, R. Yan, K. Solanki, J. Erickson, C. Chang, M. Dumontier, J. Dordick and D. McGuinness, A nanopublication framework for systems biology and drug repurposing, in: ICBO 2014 International Conference on Biomedical Ontology, Proc. of the 5th International Conference on Biomedical Ontology, Houston, Texas, USA, October 8–9, 2014, W.R. Hogan, S. Arabandi and M. Brochhausen, eds, CEUR Workshop Proceedings, Vol. 1327, 2014, pp. 90–92.
  13. Mina, 2015, Nanopublications for exposing experimental data in the life-sciences: A Huntington’s disease case study, Journal of Biomedical Semantics, 6, 5, 10.1186/2041-1480-6-5 · DOI
  14. N. Queralt-Rosinach and L.I. Furlong, DisGeNET RDF: A gene-disease association Linked Open Data resource, in: SWAT4LS 2013, Semantic Web Applications and Tools for Life Sciences, Proc. of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, Edinburgh, UK, December 10, 2013, A. Paschke, A. Burger, P. Romano, M.S. Marshall and A. Splendiani, eds, CEUR Workshop Proceedings, Vol. 1114, 2013, DisGeNET RDF Web site at http://rdf.disgenet.org/.
  15. Razick, 2008, iRefIndex: A consolidated protein interaction database with provenance, BMC Bioinformatics, 9, 405, 10.1186/1471-2105-9-405 · DOI
  16. Rebholz-Schuhmann, 2012, Text-mining solutions for biomedical research: Enabling integrative biology, Nature Reviews Genetics, 13, 829, 10.1038/nrg3337 · DOI
  17. A. Rodríguez-González, M. Martinez-Romero, M. Egaña Aranguren and M.D. Wilkinson, Nanopublishing clinical diagnoses: Tracking diagnostic knowledge base content and utilization, in: 2014 IEEE 27th International Symposium on Computer-Based Medical Systems (CBMS), 2014, pp. 335–340. · DOI
  18. P. Sernadela, P. Lopes and J.L. Oliveira, Exploring nanopublications integration in pharmacovigilance scenarios, in: 2013 IEEE 15th International Conference on e-Health Networking, Applications and Services (IEEE Healthcom 2013), Lisbon, Portugal, October 9–12th, 2013, 2013, pp. 728–730. · DOI

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Metadata

Authors
Queralt-Rosinach, N., Kuhn, T., Chichester, C., Dumontier, M., Sanz, F., & Furlong, L. I.
Venue
Semantic Web
Publisher
SAGE Publications
Published
2016-06-23
Volume
7
Issue
5
Pages
519-528
ISSN
  • 2210-4968
  • 1570-0844
DOI
10.3233/sw-150189
Cited by
19
References
0

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