publication . Article . Other literature type . 2017

AgroPortal: A vocabulary and ontology repository for agronomy

Clement Jonquet; Anne Toulet; Elizabeth Arnaud; Sophie Aubin; Esther Dzale Yeumo; Vincent Emonet; John Graybeal; Marie-Angélique Laporte; Mark A. Musen; Valeria Pesce; ...
Open Access English
  • Published: 06 Dec 2017
  • Publisher: HAL CCSD
  • Country: France
Abstract
International audience; Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications. By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain. The AgroPortal project re-uses the biomedical domain's semantic tools and insights to serve agronomy, but also foo...
Persistent Identifiers
Subjects
free text keywords: Ontologies, Controlled vocabularies, Knowledge organization systems or artifacts, Ontology repository, Metadata, Mapping, Recommendation, Semantic annotation, Agronomy, Food, Plant sciences, Biodiversity, [INFO.INFO-WB]Computer Science [cs]/Web, C30 - Documentation et information, A50 - Recherche agronomique, U10 - Méthodes mathématiques et statistiques, ontologie, vocabulaire, Banque de données, Modèle mathématique, http://aims.fao.org/aos/agrovoc/c_49845, http://aims.fao.org/aos/agrovoc/c_49855, http://aims.fao.org/aos/agrovoc/c_24833, http://aims.fao.org/aos/agrovoc/c_24199, Ontologies, Controlled vocabularies, Knowledge organization systems or artifacts, Ontology repository, Metadata, Mapping, Recommendation, Semantic annotation, Agronomy, Food, Plant sciences, Biodiversity, Ontologies;Controlled vocabularies;Knowledge organization systems or artifacts;Ontology repository;Metadata;Mapping;Recommendation;Semantic annotation;Agronomy;Food;Plant sciences;Biodiversity, Agronomy and Crop Science, Forestry, Horticulture, Computer Science Applications, Computer science, Controlled vocabulary, Knowledge organization system, Ontology (information science), Semantic Web, Simple Knowledge Organization System, computer.file_format, computer, Open Biomedical Ontologies, Agronomy, Metadata, Ontology
Funded by
EC| SIFRm
Project
SIFRm
Semantic Indexing of French Biomedical Data Resources - mobility
  • Funder: European Commission (EC)
  • Project Code: 701771
  • Funding stream: H2020 | MSCA-IF-GF
Validated by funder
Communities
Agricultural and Food Sciences
Rural Digital Europe
85 references, page 1 of 6

Goble, C., Stevens, R., 2008. State of the nation in data integration for bioinformatics. Biomed. Inf. 41, 687-693. [OpenAIRE]

Rubin, D.L., Shah, N.H., Noy, N.F., 2008. Biomedical ontologies: a functional perspective. Brief. Bioinform. 9 (1), 75-90.

Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al., 2000. Gene ontology: tool for the unification of biology. Nat. Genet. 25 (1), 25-29.

Cooper, L., Walls, R.L., Elser, J., Gandolfo, M.A., Stevenson, D.W., Smith, B., Preece, J., Athreya, B., Mungall, C.J., Rensing, S., Hiss, M., Lang, D., Reski, R., Berardini, T.Z., Li, D., Huala, E., Schaeffer, M., Menda, N., Arnaud, E., Shrestha, R., Yamazaki, Y., Jaiswal, P., 2012. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol. 54, e1.

Shrestha, R., Arnaud, E., Mauleon, R., Senger, M., Davenport, G.F., Hancock, D., Morrison, N., Bruskiewich, R., McLaren, G., 2010. Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants, vol. 2010, May.

Buttigieg, P.L., Morrison, N., Smith, B., Mungall, C.J., Lewis, S.E., 2013. The environment ontology: contextualising biological and biomedical entities. Biomed. Semantics 4, 43.

Devare, M., Aubert, C., Laporte, M.-A., Valette, L., Arnaud, E., Buttigieg, P.L., 2016. Datadriven agricultural research for development - a need for data harmonization via semantics. In: Jaiswal, P., Hoehndorf, R. (Eds.), 7th International Conference on Biomedical Ontologies, ICBO'16, vol. 1747 of CEUR Workshop Proceedings, Corvallis, Oregon, USA, pp. 2, August.

Garnier, E., Stahl, U., Laporte, M.-A., Kattge, J., Mougenot, I., Kühn, I., Laporte, B., Amiaud, B., Ahrestani, F.S., Bönisch, G., Bunker, D.E., Cornelissen, J.H.C., Díaz, S., Enquist, B.J., Gachet, S., Jaureguiberry, P., Kleyer, M., Lavorel, S., Maicher, L., PérezHarguindeguy, N., Poorter, H., Schildhauer, M., Shipley, B., Violle, C., Weiher, E., Wirth, C., Wright, I.J., Klotz, S., 2017. Towards a thesaurus of plant characteristics: an ecological contribution. Ecology 105, 298-309.

Griffiths, E., Brinkman, F., Buttigieg, P.L., Dooley, D., Hsiao, W., Hoehndorf, R., 2016. FoodON: a global farm-to-fork food ontology - the development of a universal food vocabulary. In: Jaiswal, P., Hoehndorf, R., (Eds.), 7th International Conference on Biomedical Ontologies, ICBO'16, vol. 1747 of CEUR Workshop Proceedings, Corvallis, Oregon, USA, pp. 2, August.

Musker, R., Lange, M., Hollander, A., Huber, P., Springer, N., Riggle, C., Quinn, J.F., Tomich, T.P., 2016. Towards designing an ontology encompassing the environmentagriculture-food-diet-health knowledge spectrum for food system sustainability and resilience. In: Jaiswal, P., Hoehndorf, R. (Eds.), 7th International Conference on Biomedical Ontologies, ICBO'16, vol. 1747 of CEUR Workshop Proceedings, Corvallis, Oregon, USA, pp. 5, August.

Hughes, L.M., Bao, J., Hu, Z.-L., Honavar, V., Reecy, J.M., 2014. Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species. Anim. Sci. 86, 1485-1491.

Meng, X.-X., 2012. Special issue - agriculture ontology. Integrative Agriculture, vol. 11, pp. 1, May.

Walls, R.L., Deck, J., Guralnick, R., Baskauf, S., Beaman, R., Blum, S., Bowers, S., Buttigieg, P.L., Davies, N., Endresen, D., Gandolfo, M.A., Hanner, R., Janning, A., Krishtalka, L., Matsunaga, A., Midford, P., Morrison, N., Tuama, Éamonn Ó., Schildhauer, M., Smith, B., Stucky, B.J., Thomer, A., Wieczorek, J., Whitacre, J., Wooley, J., 2014. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PLoS One 9, 13.

Wang, Y., Wang, Y., Wang, J., Yuan, Y., Zhang, Z., 2015. An ontology-based approach to integration of hilly citrus production knowledge. Comput. Electron. Agric. 113, 24-43.

Lousteau-Cazalet, C., Barakat, A., Belaud, J.-P., Buche, P., Busset, G., Charnomordic, B., Dervaux, S., Destercke, S., Dibie, J., Sablayrolles, C., Vialle, C., 2016. A decision support system for eco-efficient biorefinery process comparison using a semantic approach. Comput. Electron. Agric. 127, 351-367.

85 references, page 1 of 6
Abstract
International audience; Many vocabularies and ontologies are produced to represent and annotate agronomic data. However, those ontologies are spread out, in different formats, of different size, with different structures and from overlapping domains. Therefore, there is need for a common platform to receive and host them, align them, and enabling their use in agro-informatics applications. By reusing the National Center for Biomedical Ontologies (NCBO) BioPortal technology, we have designed AgroPortal, an ontology repository for the agronomy domain. The AgroPortal project re-uses the biomedical domain's semantic tools and insights to serve agronomy, but also foo...
Persistent Identifiers
Subjects
free text keywords: Ontologies, Controlled vocabularies, Knowledge organization systems or artifacts, Ontology repository, Metadata, Mapping, Recommendation, Semantic annotation, Agronomy, Food, Plant sciences, Biodiversity, [INFO.INFO-WB]Computer Science [cs]/Web, C30 - Documentation et information, A50 - Recherche agronomique, U10 - Méthodes mathématiques et statistiques, ontologie, vocabulaire, Banque de données, Modèle mathématique, http://aims.fao.org/aos/agrovoc/c_49845, http://aims.fao.org/aos/agrovoc/c_49855, http://aims.fao.org/aos/agrovoc/c_24833, http://aims.fao.org/aos/agrovoc/c_24199, Ontologies, Controlled vocabularies, Knowledge organization systems or artifacts, Ontology repository, Metadata, Mapping, Recommendation, Semantic annotation, Agronomy, Food, Plant sciences, Biodiversity, Ontologies;Controlled vocabularies;Knowledge organization systems or artifacts;Ontology repository;Metadata;Mapping;Recommendation;Semantic annotation;Agronomy;Food;Plant sciences;Biodiversity, Agronomy and Crop Science, Forestry, Horticulture, Computer Science Applications, Computer science, Controlled vocabulary, Knowledge organization system, Ontology (information science), Semantic Web, Simple Knowledge Organization System, computer.file_format, computer, Open Biomedical Ontologies, Agronomy, Metadata, Ontology
Funded by
EC| SIFRm
Project
SIFRm
Semantic Indexing of French Biomedical Data Resources - mobility
  • Funder: European Commission (EC)
  • Project Code: 701771
  • Funding stream: H2020 | MSCA-IF-GF
Validated by funder
Communities
Agricultural and Food Sciences
Rural Digital Europe
85 references, page 1 of 6

Goble, C., Stevens, R., 2008. State of the nation in data integration for bioinformatics. Biomed. Inf. 41, 687-693. [OpenAIRE]

Rubin, D.L., Shah, N.H., Noy, N.F., 2008. Biomedical ontologies: a functional perspective. Brief. Bioinform. 9 (1), 75-90.

Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al., 2000. Gene ontology: tool for the unification of biology. Nat. Genet. 25 (1), 25-29.

Cooper, L., Walls, R.L., Elser, J., Gandolfo, M.A., Stevenson, D.W., Smith, B., Preece, J., Athreya, B., Mungall, C.J., Rensing, S., Hiss, M., Lang, D., Reski, R., Berardini, T.Z., Li, D., Huala, E., Schaeffer, M., Menda, N., Arnaud, E., Shrestha, R., Yamazaki, Y., Jaiswal, P., 2012. The plant ontology as a tool for comparative plant anatomy and genomic analyses. Plant Cell Physiol. 54, e1.

Shrestha, R., Arnaud, E., Mauleon, R., Senger, M., Davenport, G.F., Hancock, D., Morrison, N., Bruskiewich, R., McLaren, G., 2010. Multifunctional crop trait ontology for breeders' data: field book, annotation, data discovery and semantic enrichment of the literature. AoB Plants, vol. 2010, May.

Buttigieg, P.L., Morrison, N., Smith, B., Mungall, C.J., Lewis, S.E., 2013. The environment ontology: contextualising biological and biomedical entities. Biomed. Semantics 4, 43.

Devare, M., Aubert, C., Laporte, M.-A., Valette, L., Arnaud, E., Buttigieg, P.L., 2016. Datadriven agricultural research for development - a need for data harmonization via semantics. In: Jaiswal, P., Hoehndorf, R. (Eds.), 7th International Conference on Biomedical Ontologies, ICBO'16, vol. 1747 of CEUR Workshop Proceedings, Corvallis, Oregon, USA, pp. 2, August.

Garnier, E., Stahl, U., Laporte, M.-A., Kattge, J., Mougenot, I., Kühn, I., Laporte, B., Amiaud, B., Ahrestani, F.S., Bönisch, G., Bunker, D.E., Cornelissen, J.H.C., Díaz, S., Enquist, B.J., Gachet, S., Jaureguiberry, P., Kleyer, M., Lavorel, S., Maicher, L., PérezHarguindeguy, N., Poorter, H., Schildhauer, M., Shipley, B., Violle, C., Weiher, E., Wirth, C., Wright, I.J., Klotz, S., 2017. Towards a thesaurus of plant characteristics: an ecological contribution. Ecology 105, 298-309.

Griffiths, E., Brinkman, F., Buttigieg, P.L., Dooley, D., Hsiao, W., Hoehndorf, R., 2016. FoodON: a global farm-to-fork food ontology - the development of a universal food vocabulary. In: Jaiswal, P., Hoehndorf, R., (Eds.), 7th International Conference on Biomedical Ontologies, ICBO'16, vol. 1747 of CEUR Workshop Proceedings, Corvallis, Oregon, USA, pp. 2, August.

Musker, R., Lange, M., Hollander, A., Huber, P., Springer, N., Riggle, C., Quinn, J.F., Tomich, T.P., 2016. Towards designing an ontology encompassing the environmentagriculture-food-diet-health knowledge spectrum for food system sustainability and resilience. In: Jaiswal, P., Hoehndorf, R. (Eds.), 7th International Conference on Biomedical Ontologies, ICBO'16, vol. 1747 of CEUR Workshop Proceedings, Corvallis, Oregon, USA, pp. 5, August.

Hughes, L.M., Bao, J., Hu, Z.-L., Honavar, V., Reecy, J.M., 2014. Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species. Anim. Sci. 86, 1485-1491.

Meng, X.-X., 2012. Special issue - agriculture ontology. Integrative Agriculture, vol. 11, pp. 1, May.

Walls, R.L., Deck, J., Guralnick, R., Baskauf, S., Beaman, R., Blum, S., Bowers, S., Buttigieg, P.L., Davies, N., Endresen, D., Gandolfo, M.A., Hanner, R., Janning, A., Krishtalka, L., Matsunaga, A., Midford, P., Morrison, N., Tuama, Éamonn Ó., Schildhauer, M., Smith, B., Stucky, B.J., Thomer, A., Wieczorek, J., Whitacre, J., Wooley, J., 2014. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies. PLoS One 9, 13.

Wang, Y., Wang, Y., Wang, J., Yuan, Y., Zhang, Z., 2015. An ontology-based approach to integration of hilly citrus production knowledge. Comput. Electron. Agric. 113, 24-43.

Lousteau-Cazalet, C., Barakat, A., Belaud, J.-P., Buche, P., Busset, G., Charnomordic, B., Dervaux, S., Destercke, S., Dibie, J., Sablayrolles, C., Vialle, C., 2016. A decision support system for eco-efficient biorefinery process comparison using a semantic approach. Comput. Electron. Agric. 127, 351-367.

85 references, page 1 of 6
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