publication . Preprint . Article . 2020

39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition

Caterina Caracciolo; Sophie Aubin; Clement Jonquet; Emna Amdouni; Romain David; Leyla Garcia; Brandon Whitehead; Catherine Roussey; Armando Stellato; Ferdinando Villa;
Open Access English
  • Published: 11 Dec 2020
Abstract
In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered researchers and practitioners at the crossing point between information technology and agricultural science, to study all aspects in the life cycle of semantic resources: Conceptualization, edition, sharing, standardization, services, alignment, long term support. First, the working group realized a landscape study, a ...
Persistent Identifiers
Subjects
free text keywords: Quantitative Biology - Other Quantitative Biology, Computer Science - Databases, agrifood data, fair data, semantics, semantic resources, ontology, vocabulary, terminology, thesauri, ontology repository, terminology service, Agricultural robots, Agriculture, Data Science, Life cycle, Nutrition, Agricultural science, Crossing point, Data interoperability, Data production, Research data, Semantic technologies, Working groups, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDE.ES]Environmental Sciences/Environmental and Society, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Semantic web, agricultural data, agrifood data; FAIR data; semantics; semantic resources; ontology; vocabulary; terminology; thesauri; ontology repository; terminology service, Computer Science (miscellaneous), Computer Science Applications, lcsh:Science (General), lcsh:Q1-390, Reuse, Standardization, Conceptualization, Semantics, Ontology (information science), Knowledge management, business.industry, business, Use case, Semantic technology, Computer science, Information technology
Funded by
ANR| PHENOME
Project
PHENOME
Centre français de phénomique végétale
  • Funder: French National Research Agency (ANR) (ANR)
  • Project Code: ANR-11-INBS-0012
,
EC| EOSC-Life
Project
EOSC-Life
Providing an open collaborative space for digital biology in Europe
  • Funder: European Commission (EC)
  • Project Code: 824087
  • Funding stream: H2020 | RIA
Validated by funder
,
EC| RDA Europe 4.0
Project
RDA Europe 4.0
The European plug-in to the global Research Data Alliance
  • Funder: European Commission (EC)
  • Project Code: 777388
  • Funding stream: H2020 | CSA
,
EC| EPPN2020
Project
EPPN2020
European Plant Phenotyping Network 2020
  • Funder: European Commission (EC)
  • Project Code: 731013
  • Funding stream: H2020 | RIA
Validated by funder
,
ANR| D2KAB
Project
D2KAB
Data to Knowledge in Agriculture and Biodiversity
  • Funder: French National Research Agency (ANR) (ANR)
  • Project Code: ANR-18-CE23-0017
Communities
Agricultural and Food Sciences
Research Data AllianceRDA Projects: RDA Europe 4.0
Rural Digital Europe
36 references, page 1 of 3

AgroPortal, release 2.0, Spet. 2020.

Aubin, S, Caracciolo, C, Keizer, J and RDA Agrisemantics, WG. 2017a. Agrisemantics: vision for an infrastructure for semantic-based interoperability of agricultural data. DOI: https://doi.org/10.7490/ f1000research.1114967.1

Aubin, S, Caracciolo, C and Whitehead, B. 2018. Uses and Needs of Semantic Resources in the Area of Agriculture. RDA Agrisemantics Working Group. DOI: https://doi.org/10.5281/zenodo.3700849

Aubin, S, Caracciolo, C and Zervas, P. 2017b. Landscaping the Use of Semantics to Enhance the Interoperability of Agricultural Data. RDA Agrisemantics Working Group. DOI: https://doi.org/10.5281/ zenodo.3697332

Baker, T, Caracciolo, C, Doroszenko, A, Finch, L, Suominen, O and Suri, S. 2017. The Global Agricultural Concept Scheme and Agrisemantics. International Conference on Dublin Core and Metadata Applications 0, 14-15.

Caliper. [WWW Document], n.d. URL http://stats-class.fao.uniroma2.it/caliper/ (accessed 1.27.20).

Caracciolo, C, Aubin, S and Whitehead, B. 2019a. The Agrisemantics recommendations to improve data interoperability in agriculture. F1000Research 8. DOI: https://doi.org/10.7490/f1000research.1117569.1

Caracciolo, C, Aubin, S, Whitehead, B and Zervas, P. 2019b. Semantics for Data in Agriculture: A Community-Based Wish List. In: Garoufallou, E, Sartori, F, Siatri, R and Zervas, M (Eds.), Metadata and Semantic Research. MTSR 2018. Communications in Computer and Information Science. Cham: Springer, pp. 340-345. DOI: https://doi.org/10.1007/978-3-030-14401-2_32

CIAT. n.d. CGIAR BIG DATA Platform [WWW Document]. CGIAR Platform for Big Data in Agriculture. URL https://bigdata.cgiar.org/ (accessed 4.15.20).

Crosson, P, Shalloo, L, O'Brien, D, Lanigan, GJ, Foley, PA, Boland, TM and Kenny, DA. 2011. A review of whole farm systems models of greenhouse gas emissions from beef and dairy cattle production systems. Animal Feed Science and Technology, Special Issue: Greenhouse Gases in Animal Agriculture - Finding a Balance between Food and Emissions 166-167, 29-45. DOI: https://doi.org/10.1016/j.anifeedsci.2011.04.001

David, R, Mabile, L, Specht, A, Sarah, S, Thomsen, M, Yahia, M, Dollé, L, Jonquet, C, Bailo, D, Bravo, E, Gachet, S, Gunderman, H, Hollebecq, J-E, Ioannidis, V, Jacob, D, Le Bras, Y, Lerigoleur, E, CambonThomsen, A and Research Data Alliance - SHAring Reward and Credit (SHARC) Interest Group, TRD. 2020. FAIRness Literacy: The Achilles' Heel of Applying FAIR Principles. Data Science Journal, 19(1), p.32. DOI: https://doi.org/10.5334/dsj-2020-032

GO FAIR. n.d. GO FAIR [WWW Document]. GO FAIR. URL https://www.go-fair.org/ (accessed 1.27.20).

Harper, L, Campbell, J, Cannon, EKS, Jung, S, Poelchau, M, Walls, R, Andorf, C, Arnaud, E, Berardini, TZ, Birkett, C, Cannon, S, Carson, J, Condon, B, Cooper, L, Dunn, N, Elsik, CG, Farmer, A, Ficklin, SP, Grant, D, Grau, E, Herndon, N, Hu, Z-L, Humann, J, Jaiswal, P, Jonquet, C, Laporte, M-A, Larmande, P, Lazo, G, McCarthy, F, Menda, N, Mungall, CJ, Munoz-Torres, MC, Naithani, S, Nelson, R, Nesdill, D, Park, C, Reecy, J, Reiser, L, Sanderson, L-A, Sen, TZ, Staton, M, Subramaniam, S, Tello-Ruiz, MK, Unda, V, Unni, D, Wang, L, Ware, D, Wegrzyn, J, Williams, J, Woodhouse, M, Yu, J and Main, D. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford) 2018. DOI: https://doi.org/10.1093/database/bay088

Johnston, AE and Poulton, PR. 2018. The importance of long-term experiments in agriculture: their management to ensure continued crop production and soil fertility; the Rothamsted experience. Eur J Soil Sci, 69: 113-125. DOI: https://doi.org/10.1111/ejss.12521 [OpenAIRE]

Jonquet, C, Toulet, A, Arnaud, E, Aubin, S, Dzalé Yeumo, E, Emonet, V, Graybeal, J, Laporte, M-A, Musen, MA, Pesce, V and Larmande, P. 2018a. AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture, 144: 126-143. DOI: https://doi.org/10.1016/j.compag.2017.10.012 [OpenAIRE]

36 references, page 1 of 3
Abstract
In this paper, we report on the outputs and adoption of the Agrisemantics Working Group of the Research Data Alliance (RDA), consisting of a set of recommendations to facilitate the adoption of semantic technologies and methods for the purpose of data interoperability in the field of agriculture and nutrition. From 2016 to 2019, the group gathered researchers and practitioners at the crossing point between information technology and agricultural science, to study all aspects in the life cycle of semantic resources: Conceptualization, edition, sharing, standardization, services, alignment, long term support. First, the working group realized a landscape study, a ...
Persistent Identifiers
Subjects
free text keywords: Quantitative Biology - Other Quantitative Biology, Computer Science - Databases, agrifood data, fair data, semantics, semantic resources, ontology, vocabulary, terminology, thesauri, ontology repository, terminology service, Agricultural robots, Agriculture, Data Science, Life cycle, Nutrition, Agricultural science, Crossing point, Data interoperability, Data production, Research data, Semantic technologies, Working groups, [INFO.INFO-ET]Computer Science [cs]/Emerging Technologies [cs.ET], [INFO.INFO-DB]Computer Science [cs]/Databases [cs.DB], [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, [SDE.ES]Environmental Sciences/Environmental and Society, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Semantic web, agricultural data, agrifood data; FAIR data; semantics; semantic resources; ontology; vocabulary; terminology; thesauri; ontology repository; terminology service, Computer Science (miscellaneous), Computer Science Applications, lcsh:Science (General), lcsh:Q1-390, Reuse, Standardization, Conceptualization, Semantics, Ontology (information science), Knowledge management, business.industry, business, Use case, Semantic technology, Computer science, Information technology
Funded by
ANR| PHENOME
Project
PHENOME
Centre français de phénomique végétale
  • Funder: French National Research Agency (ANR) (ANR)
  • Project Code: ANR-11-INBS-0012
,
EC| EOSC-Life
Project
EOSC-Life
Providing an open collaborative space for digital biology in Europe
  • Funder: European Commission (EC)
  • Project Code: 824087
  • Funding stream: H2020 | RIA
Validated by funder
,
EC| RDA Europe 4.0
Project
RDA Europe 4.0
The European plug-in to the global Research Data Alliance
  • Funder: European Commission (EC)
  • Project Code: 777388
  • Funding stream: H2020 | CSA
,
EC| EPPN2020
Project
EPPN2020
European Plant Phenotyping Network 2020
  • Funder: European Commission (EC)
  • Project Code: 731013
  • Funding stream: H2020 | RIA
Validated by funder
,
ANR| D2KAB
Project
D2KAB
Data to Knowledge in Agriculture and Biodiversity
  • Funder: French National Research Agency (ANR) (ANR)
  • Project Code: ANR-18-CE23-0017
Communities
Agricultural and Food Sciences
Research Data AllianceRDA Projects: RDA Europe 4.0
Rural Digital Europe
36 references, page 1 of 3

AgroPortal, release 2.0, Spet. 2020.

Aubin, S, Caracciolo, C, Keizer, J and RDA Agrisemantics, WG. 2017a. Agrisemantics: vision for an infrastructure for semantic-based interoperability of agricultural data. DOI: https://doi.org/10.7490/ f1000research.1114967.1

Aubin, S, Caracciolo, C and Whitehead, B. 2018. Uses and Needs of Semantic Resources in the Area of Agriculture. RDA Agrisemantics Working Group. DOI: https://doi.org/10.5281/zenodo.3700849

Aubin, S, Caracciolo, C and Zervas, P. 2017b. Landscaping the Use of Semantics to Enhance the Interoperability of Agricultural Data. RDA Agrisemantics Working Group. DOI: https://doi.org/10.5281/ zenodo.3697332

Baker, T, Caracciolo, C, Doroszenko, A, Finch, L, Suominen, O and Suri, S. 2017. The Global Agricultural Concept Scheme and Agrisemantics. International Conference on Dublin Core and Metadata Applications 0, 14-15.

Caliper. [WWW Document], n.d. URL http://stats-class.fao.uniroma2.it/caliper/ (accessed 1.27.20).

Caracciolo, C, Aubin, S and Whitehead, B. 2019a. The Agrisemantics recommendations to improve data interoperability in agriculture. F1000Research 8. DOI: https://doi.org/10.7490/f1000research.1117569.1

Caracciolo, C, Aubin, S, Whitehead, B and Zervas, P. 2019b. Semantics for Data in Agriculture: A Community-Based Wish List. In: Garoufallou, E, Sartori, F, Siatri, R and Zervas, M (Eds.), Metadata and Semantic Research. MTSR 2018. Communications in Computer and Information Science. Cham: Springer, pp. 340-345. DOI: https://doi.org/10.1007/978-3-030-14401-2_32

CIAT. n.d. CGIAR BIG DATA Platform [WWW Document]. CGIAR Platform for Big Data in Agriculture. URL https://bigdata.cgiar.org/ (accessed 4.15.20).

Crosson, P, Shalloo, L, O'Brien, D, Lanigan, GJ, Foley, PA, Boland, TM and Kenny, DA. 2011. A review of whole farm systems models of greenhouse gas emissions from beef and dairy cattle production systems. Animal Feed Science and Technology, Special Issue: Greenhouse Gases in Animal Agriculture - Finding a Balance between Food and Emissions 166-167, 29-45. DOI: https://doi.org/10.1016/j.anifeedsci.2011.04.001

David, R, Mabile, L, Specht, A, Sarah, S, Thomsen, M, Yahia, M, Dollé, L, Jonquet, C, Bailo, D, Bravo, E, Gachet, S, Gunderman, H, Hollebecq, J-E, Ioannidis, V, Jacob, D, Le Bras, Y, Lerigoleur, E, CambonThomsen, A and Research Data Alliance - SHAring Reward and Credit (SHARC) Interest Group, TRD. 2020. FAIRness Literacy: The Achilles' Heel of Applying FAIR Principles. Data Science Journal, 19(1), p.32. DOI: https://doi.org/10.5334/dsj-2020-032

GO FAIR. n.d. GO FAIR [WWW Document]. GO FAIR. URL https://www.go-fair.org/ (accessed 1.27.20).

Harper, L, Campbell, J, Cannon, EKS, Jung, S, Poelchau, M, Walls, R, Andorf, C, Arnaud, E, Berardini, TZ, Birkett, C, Cannon, S, Carson, J, Condon, B, Cooper, L, Dunn, N, Elsik, CG, Farmer, A, Ficklin, SP, Grant, D, Grau, E, Herndon, N, Hu, Z-L, Humann, J, Jaiswal, P, Jonquet, C, Laporte, M-A, Larmande, P, Lazo, G, McCarthy, F, Menda, N, Mungall, CJ, Munoz-Torres, MC, Naithani, S, Nelson, R, Nesdill, D, Park, C, Reecy, J, Reiser, L, Sanderson, L-A, Sen, TZ, Staton, M, Subramaniam, S, Tello-Ruiz, MK, Unda, V, Unni, D, Wang, L, Ware, D, Wegrzyn, J, Williams, J, Woodhouse, M, Yu, J and Main, D. 2018. AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database (Oxford) 2018. DOI: https://doi.org/10.1093/database/bay088

Johnston, AE and Poulton, PR. 2018. The importance of long-term experiments in agriculture: their management to ensure continued crop production and soil fertility; the Rothamsted experience. Eur J Soil Sci, 69: 113-125. DOI: https://doi.org/10.1111/ejss.12521 [OpenAIRE]

Jonquet, C, Toulet, A, Arnaud, E, Aubin, S, Dzalé Yeumo, E, Emonet, V, Graybeal, J, Laporte, M-A, Musen, MA, Pesce, V and Larmande, P. 2018a. AgroPortal: A vocabulary and ontology repository for agronomy. Computers and Electronics in Agriculture, 144: 126-143. DOI: https://doi.org/10.1016/j.compag.2017.10.012 [OpenAIRE]

36 references, page 1 of 3
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