Have a personal or library account? Click to login
Enhancing the FAIRness of Arctic Research Data Through Semantic Annotation Cover

Enhancing the FAIRness of Arctic Research Data Through Semantic Annotation

Open Access
|Jan 2024

References

  1. 1Aguado-de-Cea, G, Montiel-Ponsada, E, Poveda-Villalón, M and Giraldo-Pasmin, O. 2015. Lexicalizing ontologies: The issues behind the labels. Procedia: Social and Behavioral Sciences, 212(2015): 151158. DOI: 10.1080/17538947.2014.1003106
  2. 2Ashburner, M, Ball, CA, Blake, JA, Botstein, D, Butler, H, Cherry, JM, Davis, AP, Dolinski, K, Dwight, SS, Eppig, JT and Harris, MA. 2000. Gene ontology: tool for the unification of biology. Nature genetics, 25(1): 2529. DOI: 10.1038/75556
  3. 3Baumann, P, Mazzetti, P, Ungar, J, Barbera, R, Barboni, D, Beccati, A, Bigagli, L, Boldrini, E, Bruno, R, Calanducci, A and others. 2016. Big data analytics for earth sciences: The EarthServer approach. International Journal of Digital Earth, 9(1): 329. DOI: 10.1080/17538947.2014.1003106
  4. 4Berners-Lee, T, Hendler, J and Lassila, O. 2001. The semantic web. Scientific American, 284(5): 3443. DOI: 10.1038/scientificamerican0501-34
  5. 5Brickley, D and Guha, RV. 2014. RDF Schema 1.1. Available at https://www.w3.org/TR/rdf-schema/ [Last accessed 11 January 2021].
  6. 6Buttigieg, PL, Morrison, N, Smith, B, Mungall, CJ, Lewis, SE and Envo Consortium. 2013. The environment ontology: Contextualising biological and biomedical entities. Journal of Biomedical Semantics, 4(1): 43. DOI: 10.1186/2041-1480-4-43
  7. 7Buttigieg, PL, Pafilis, E, Lewis, SE, Schildhauer, MP, Walls, RL and Mungall, CJ. 2016. The environment ontology in 2016: Bridging domains with increased scope, semantic density, and interoperation. Journal of Biomedical Semantics, 7(1): 57. DOI: 10.1186/s13326-016-0097-6
  8. 8Chapin, FS, McFarland, J, McGuire, AD, Euskirchen, ES, Ruess, RW and Kielland, K. 2009. The changing global carbon cycle: Linking plant–soil carbon dynamics to global consequences. Journal of Ecology, 97: 840850. DOI: 10.1111/j.1365-2745.2009.01529.x
  9. 9Chapin, FS, Woodwell, GM, Randerson, JT, Rastetter, EB, Lovett, GM, Baldocchi, DD, Clark, DA, Harmon, ME, Schimel, DS, Valentini, R and others. 2006. Reconciling carbon-cycle concepts, terminology, and methods. Ecosystems, 9(7): 10411050. DOI: 10.1007/s10021-005-0105-7
  10. 10Chong, S, Jones, M, Mecum, B and O’Brien, M. 2021. Arctic semantics GitHub repository (Supplement to “Enhancing the FAIRness of Arctic research data” in IJDC release) [software]. Available from. https://archive.softwareheritage.org/swh:1:rel:b615ca4601ae230cdefa8035b708384d6fce3d06.
  11. 11Cox, SJ, Gonzalez-Beltran, AN, Magagna, B and Marinescu, MC. 2021. Ten simple rules for making a vocabulary FAIR. PLoS Computational Biology, 17(6). DOI: 10.1371/journal.pcbi.1009041
  12. 12Cyganiak, R, Wood, D and Lanthaler, M. 2014. RDF 1.1 Concepts and Abstract Syntax. Available at https://www.w3.org/TR/rdf11-concepts/ [Last accessed January 13, 2021].
  13. 13Decker, S, Melnik, S, Van Harmelen, F, Fensel, D, Klein, M, Broekstra, J, Erdmann, M and Horrocks, I. 2000. The semantic web: The roles of XML and RDF. IEEE Internet Computing, 4(5): 6373. DOI: 10.1109/4236.877487
  14. 14Dunning, A, De Smaele, M and Böhmer, J. 2017. Are the fair data principles fair? International Journal of Digital Curation, 12(2): 177195. DOI: 10.2218/ijdc.v12i2.567
  15. 15Faria, D, Pesquita, C, Mott, I, Martins, C, Couto, F and Cruz, I. 2018. Tackling the challenges of matching biomedical ontologies. Journal of Biomedical Semantics, 9: 4. DOI: 10.1002/ece3.9592
  16. 16Gries, C, Hanson, PC, O’Brien, M, Servilla, M, Vanderbilt, K and Waide, R. 2023. The environmental data initiative: Connecting the past to the future through data reuse. Ecology and Evolution, 13(1): e9592. DOI: 10.1002/ece3.9592
  17. 17Harden, JW, Hugelius, G, Ahlström, A, Blankinship, JC, Bond-Lamberty, B, Lawrence, CR, Loisel, J, Malhotra, A, Jackson, RB, Ogle, S and others. 2018. Networking our science to characterize the state, vulnerabilities, and management opportunities of soil organic matter. Global Change Biology, 24(2): e705e718. DOI: 10.1111/gcb.13896
  18. 18Hugo, W, Le Franc, Y, Coen, G, Parland-von Essen, J and Bonino, L. 2020. D2.5 FAIR Semantics Recommendations Second Iteration (1.0). Zenodo. DOI: 10.5281/zenodo.5362010
  19. 19Jones, MB, O’Brien, M, Mecum, B, Boettiger, C, Schildhauer, M, Maier, M, Whiteaker, T, Earl, S and Chong, S. 2019. Ecological Metadata Language (version 2.2.0). KNB Data Repository. DOI: 10.5063/F11834T2
  20. 20Jovanović, J and Bagheri, E. 2017. Semantic annotation in biomedicine: the current landscape. Journal of Biomedical Semantics, 8(1): 118. DOI: 10.1186/s13326-017-0153-x
  21. 21Katz, SL, Barnas, KA, Diaz, M and Hampton, SE. 2019. Data system design alters meaning in ecological data: Salmon habitat restoration across the US Pacific Northwest. Ecosphere, 10(11): e02920. DOI: 10.1002/ecs2.2920
  22. 22Kempler, S and Mathews, T. 2017. Earth science data analytics: Definitions, techniques and skills. Data Science Journal, 16: Article 6. DOI: 10.5334/dsj-2017-006
  23. 23Krovetz, R. 1997. Homonymy and polysemy in information retrieval. In: 35th Annual Meeting of the Association for Computational Linguistics and 8th Conference of the European Chapter of the Association for Computational Linguistics. Madrid, Spain on 7–12 July 1997, pp. 7279. DOI: 10.3115/976909.979627
  24. 24Krovetz, R and Croft, WB. 1992. Lexical ambiguity and information retrieval. ACM Transactions on Information Systems, 10(2): 115141. DOI: 10.1145/146802.146810
  25. 25Liao, X and Zhao, Z. 2019. Unsupervised approaches for textual semantic annotation, a survey. ACM Computing Surveys (CSUR), 52(4): 145. DOI: 10.1145/3324473
  26. 26Madin, JS, Bowers, S, Schildhauer, MP and Jones, MB. 2008. Advancing ecological research with ontologies. Trends in Ecology & Evolution, 23(3): 159168. DOI: 10.1016/j.tree.2007.11.007
  27. 27Madin, J, Bowers, S, Schildhauer, M, Krivov, S, Pennington, D and Villa, F. 2007. An ontology for describing and synthesizing ecological observation data. Ecological Informatics, 2(3): 279296. DOI: 10.1016/j.ecoinf.2007.05.004
  28. 28Magagna, B, Schindler, S, Stoica, M, Moncoiffe, G, Devaraju, A and Pamment, A. 2021. I-ADOPT Framework ontology. Retrieved from https://w3id.org/iadopt/ont/0.9.1.
  29. 29Mantovani, A, Piana, F and Lombardo, V. 2020. Ontology-driven representation of knowledge for geological maps. Computers & Geosciences, 139: 104446. DOI: 10.1016/j.cageo.2020.104446
  30. 30McGuinness, DL and Van Harmelen, F. 2004. OWL web ontology language overview. W3C Recommendation, 10(10): 2004.
  31. 31Miles, A and Bechhofer, S. 2009. SKOS simple knowledge organization system reference. Available at https://www.w3.org/TR/2009/REC-skos-reference-20090818/ [Last accessed 11 January 2021].
  32. 32O’Brien, M, Jones, M, Schildhauer, M, Hou, S, Mecum, B, McCusker, J and McGuinness, D. 2023. (Dataset) Results of semantic queries for “carbon cycling” for datasets in the DataONE catalog ver 2. Environmental Data Initiative. DOI: 10.6073/pasta/c93d87c2000715eaa2f70d079965c6a5 (Accessed 2023-03-29).
  33. 33Open Biological and Biomedical Ontologies Technical Working Group. 2020. Principles: Overview. Available at http://www.obofoundry.org/principles/fp-000-summary.html [Last accessed 23 September 2020].
  34. 34Rogers, FB. 1963. Medical subject headings. Bulletin of the Medical Library Association, 51: 114116.
  35. 35Schildhauer, M. (n.d.) Semantic annotations. Available at https://arcticdata.io/semantic-annotations [Last accessed 19 October 2023].
  36. 36Schildhauer, M, Chong, S, O’Brien, M, Mecum, B and Jones, MB. 2019. Semantic approaches to enhancing data findability and interoperability in the NSF DataONE and Arctic Data Center Data Repositories. American Geophysical Union Fall Meeting, 2019, IN22C-19. Available at https://ui.adsabs.harvard.edu/abs/2019AGUFMIN22C..19S/abstract [Last accessed 31 August 2020].
  37. 37Smith, B. 2012. Ontology. In: Hurtado, G and Nudler, O (eds.), The Furniture of the World: Essays in Ontology and Metaphysics. New York: Brill Rodopi. pp. 4768. DOI: 10.1163/9789401207799_005
  38. 38Vanderbilt, KL, Gries, C and O’Brien, MC. 2020. Annotating metadata to improve data discovery and reuse. In: 2020 ESA Annual Meeting, 3–6 August. Ecological Society of America. Available at https://eco.confex.com/eco/2020/meetingapp.cgi/Paper/85318 [Last accessed 31 August 2020].
  39. 39Wilkinson, MD, Dumontier, M, Aalbersberg, IJ, Appleton, G, Axton, M, Baak, A, Blomberg, N, Boiten, J-W, da Silva Santos, LB, Bourne, PE and others. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data, 3(1): 19. DOI: 10.1038/sdata.2016.18
Language: English
Submitted on: Apr 5, 2023
Accepted on: Nov 28, 2023
Published on: Jan 17, 2024
Published by: Ubiquity Press
In partnership with: Paradigm Publishing Services
Publication frequency: 1 issue per year

© 2024 Steven S. Chong, Mark Schildhauer, Margaret O’Brien, Bryce Mecum, Matthew B. Jones, published by Ubiquity Press
This work is licensed under the Creative Commons Attribution 4.0 License.