Agriculture Data Platform – Institutional Data Repository – Selected Aspects

Michal StočesJiří VaněkJan JarolímekVojtěch NovákJan MasnerPavel ŠimekEva KánskáMartin HavránekKarel KubataVladimir Voral

DOI 10.7160/aol.2023.150409
No 4/2023, December
pp. 127-133

Stočes, M., Vaněk, J., Jarolímek, J., Novák, V., Masner, J., Šimek, P., Kánská, E., Havránek, M., Kubata, K. and Voral, V. (2023) "Agriculture Data Platform – Institutional Data Repository – Selected Aspects", AGRIS on-line Papers in Economics and Informatics, Vol. 15, No. 4, pp. 127-133. ISSN 1804-1930. DOI 10.7160/aol.2023.150409.

Abstract

This paper presents selected aspects of a data platform to store agricultural data. It analyses the key user and system requirements for the data platform. The presented aspects were identified through a literature review, interviews and discussions with selected data experts and researchers and future users of the platform. The following issues of the data platform are discussed in the paper: architecture, data types, data source types, metadata, disciplinary interfaces, data sharing, data reusability, Open Science, FAIR data principles, and further data processing options. Part of the knowledge from this article was used in the design and implementation of the Institutional Data Repository called Data Management Platform (DaMP.) CZU (Czech University of Life Sciences Prague) (OPENAI, 2023).

Keywords

Data models, data modelling, metadata, data sharing, open science, FAIR data principles, data platform, agriculture data, life sciences, institutional data repositories, data process, DOI, FAIR data.

References

  1. Burgelman, J. C. (2021) "Politics and Open Science: How the European Open Science Cloud Became Reality (the Untold Story)", Data Intelligence, Vol. 3, No. 1, No. 5-19. E-ISSN 2641-435X. DOI 10.1162/DINT_A_00069.
  2. David, A., Barbié, V., Attimonelli, M., Preste, R., Makkonen, E., Marjonen, H., Lindstedt, M., Kristiansson, K., Hunt, S. E., Cunningham, F., Lappalainen, I., and Sternberg, M. J. E. (2020) "Annotation and curation of human genomic variations: an ELIXIR Implementation Study", F1000Research 2020 9:1207, Vol. 9, No. 1207. ISSN 2046-1402. DOI 10.12688/f1000research.24427.1.
  3. Gomes, D. G. E., Pottier, P., Crystal-Ornelas, R., Hudgins, E. J., Foroughirad, V., Sánchez-Reyes, L. L., Turba, R., Martinez, A. P., Moreau, D., Bertram, M. G., Cooper A. Smout, C. A. and Gaynor, K. M. (2022) "Why don't we share data and code? Perceived barriers and benefits to public archiving practices", Proceedings of the Royal Society B: Biological Sciences 2022, Vol. 289, No. 1987. ISSN 0962-8452. DOI 10.1098/rspb.2022.1113.
  4. Kalendralis, P., Sloep, M., van Soest, J., Dekker, A. and Fijten, R. (2021) "Making radiotherapy more efficient with FAIR data", Physica Medica, Vol. 82, pp. 158-162. E-ISSN 1724-191X, ISSN 1120-1797. DOI 10.1016/j.ejmp.2021.01.083.
  5. Marešová, P., Jedlička, P., Soukal, I. and Novotný, J. (2019) "Open Science, Open Research Data and some Open Questions", Hradec Economic Days 2019, pp. 174-181. ISBN 978-80-7435-736-7. DOI 10.36689/uhk/hed/2019-02-017.
  6. Merton, R. K. (1973) "The Normative Structure of Science", In: Storer, N. W. (ed.) " The Sociology of Science: Theoretical and Empirical Investigations, p. 267-278. Chicago: University of Chicago Press. ISBN 0-226-52091-9.
  7. Novotný, J. (2019) "Open science, open research data and some open questions", Hradec Economic Days, Vol. 2, pp. 174-181. ISBN 978-80-7435-736-7.
  8. OPENAI (2023) "ChatGPT-4. AI program". [Online]. Available: https://openai.com/blog/chatgpt. [Accessed: Nov.16, 2023].
  9. Papoutsoglou, E. A., Faria, D., Arend, D., Arnaud, E., Athanasiadis, I. N., Chaves, I., Coppens, F., Cornut, G., Costa, B. V., Ćwiek-Kupczyńska, H., Droesbeke, B., Finkers, R., Gruden, K., Junker, A., King, G. J., Krajewski, P., Lange, M., Laporte, M. A., Michotey, C., Oppermann, M., Ostler, R., Poorter, H., Ramirez-Gonzalez, R., Ramšak, Ž., Reif, J. C., Rocca-Serra, P., Sansone, S.-A., Scholz, U., Tardieu, F., Uauy, C., Usadel, B., Visser, R. G. F., Weise, S., Kersey, P. J., Miguel, C. M., Adam-Blondon, A.-F. and Pommier, C. (2020) "Enabling reusability of plant phenomic datasets with MIAPPE 1.1", New Phytologist, Vol. 227, No. 1, pp. 260-273. ISSN 0028-646X. DOI 10.1111/NPH.16544.
  10. Prodan, R., Kimovski, D., Bartolini, A., Cochez, M., Iosup, A., Kharlamov, E., Rozanec, J., Vasiliu, L. and Varbanescu, A. L. (2022) "Towards Extreme and Sustainable Graph Processing for Urgent Societal Challenges in Europe", Proceedings - 2022 IEEE Cloud Summit, 20-21 Dec., 2022, pp. 23-30. ISSN 2330-2186. DOI 10.1109/cloudsummit54781.2022.00010.
  11. Sansone, S. A., Rocca-Serra, P., Field, D., Maguire, E., Taylor, C., Hofmann, O., Fang, H., Neumann, S., Tong, W., Amaral-Zettler, L., Begley, K., Booth, T., Bougueleret, L., Burns, G., Chapman, B., Clark, T., Coleman, L. A., Copeland, J., Das, S., … Hide, W. (2012) "Toward interoperable bioscience data", Nature Genetics, Vol. 44, No. 2, pp. 121-126. ISSN 1061-4036. DOI 10.1038/ng.1054.
  12. Agriculture Data Platform – Institutional Data Repository – Selected Aspects [133] [12] Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O. E., Birkett, C., Calaminos, V. C., Carceller, P., Cornut, G., Vasques Costa, B., Edwards, J. D., Finkers, R., Yanxin Gao, S., Ghaffar, M., Glaser, P., Guignon, V., Hok, P., Kilian, A., … Wren, J. (2019) "BrAPI - An application programming interface for plant breeding applications", Bioinformatics, Vol. 35, No. 20, pp. 4147–4155. ISSN 1367-4811. DOI 10.1093/bioinformatics/btz190.
  13. Stočes, M., Šilerová, E., Vaněk, J., Jarolímek, J. and Šimek, P. (2018) "Možnosti využití otevřených dat v sektoru cukr – cukrová řepa", Listy cukrovarnické a řepařské, Vol. 134, No. 3, pp. 117-121. ISSN 1210-3306. (In Czech).
  14. Thoegersen, J. L. and Borlund, P. (2021) "Researcher attitudes toward data sharing in public data repositories: A Meta-evaluation of studies on researcher data sharing", Journal of Documentation, Vol. 78, No. 7, pp. 1-17. ISSN 0022-0418. DOI 10.1108/JD-01-2021-0015.
  15. Tzanova, S. (2020) "Changes in academic libraries in the era of Open Science", Education for Information, Vol. 36, No. 03, pp. 281-299. ISSN 1465-3400. DOI 10.3233/EFI-190259.
  16. UNESCO (n.d.) "Implementation of the UNESCO Recommendation on Open Science" [Online], Available: https://www.unesco.org/en/open-science/implementation [Accessed: 20 Apr. 20, 2023].
  17. Wilkinson, M. D., Dumontier, M., Aalbersberg, I. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J. W., da Silva Santos, L. B., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R. Gonzalez-Beltran, A., Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., C ’t Hoen, P. A., Hooft, R., Kuhn, T., Kok, R., Kok, van Schaik, R., Sansone, S.-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Jun Zhao, J. and Mons, B. (2016) "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, Vol. 3, No. 1, pp. 1-9. ISSN 2045-2322. DOI 10.1038/sdata.2016.18.

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