Theme Co0lDB - Collection, management and dissemination of collaborative data in ecology and botany


The collection, management and validation of botanical data, which are often complex and heterogeneous, are crucial for many studies and their resulting applications. Currently, in ecology and botany, data aggregation methods are (i) based on individual solutions for which the implementation of collaborative work and sharing are difficult, (ii) based on very inclusive solutions in centralized and static infrastructures (cf. dedicated information systems) in which the data are difficult to re-use for other studies (loss of control, data model unsuitable, etc.). The objective of our research is to enable and/or facilitate the generation and exploitation of new datasets, through new methods and innovative tools for researchers and the general public.

Scientific objective

To develop participatory (citizen science) computer methods to facilitate the creation, exploration, and use of ecological and botanical databases.


Pooling and disseminating methods and software should make it possible to use more sources of data produced by research but also by the general public that were previously inaccessible due to the lack of appropriate ways to manage and disseminate the data. The mobilization of these novel big data sources should make it possible to:

  •  create collaborative datasets;
  •  implement innovative systems for information exploration (visual similarities, multi-criteria research, learning classification), and to develop expert systems to contribute to plant identification and ecological monitoring;
  •  collaboratively validate data to make it easy to publish;
  •  manage distributed data with the aim of facilitating exchanges between stakeholders.

This program is based on our experience in the field of biodiversity informatics (applied to both temperate and tropical floras, and cultivated and natural floras). It has no specific geographical focus, although for several years we have exchanged with collaborators in Europe, South America, the Indian Ocean and Oceania. Our aim is to operate, test and produce advanced research on “big data” in order to meet to the new expectations of the scientific community in this field of plant ecology and botany.

Expected results

  •  The development of software infrastructures to facilitate exploration, collection, management, validation and dissemination of large datasets in botany and ecology.
  •  National and international collaborations with different research and technical institutes.

Scientific projects

Acronym Title Duration
MIKOKOMikoko: Conservation and resilience of Kenya’s mangrove forests2019 - 2021
WEEDELECRobot de désherbage localisé par procédé électrique haute tension combiné avec une gestion prédictive par vision hyper-spectrale et post-évaluation par drone2018 - 2021
FLORIS'TICFloris'tic2015 - 2018
ARCHIWOODMorphologie végétale, anatomie et architecture des espèces endémiques de bois à Madagascar2014 - 2016
E-RECOLNATValorisation de 350 ans de collections d'histoire naturelle : une plateforme numérique pour l'environnement et la société2013 - 2019
WIKWIOWeed Identification and Knowledge in the Western Indian Ocean2013 - 2016
PL@NTNETObservation et identification interactive des plantes2009 - 2013

Major publications

All major publications 2019
  • A. Joly, H. Goëau, P. Bonnet, V. Bakic, J. Barbe, S. Selmi, I. Yahiaoui, J. Carré, , E. Mouysset, J.-F. Molino, N. Boujemaa, D. Barthélémy, 2014. Interactive plant identification based on social image data. Ecological Informatics, 23 : 22-34. [Editor link]
  • Joly A., Goëau H., Glotin H., Spampinato C., Bonnet P., Vellinga W.-P., Planque R., Rauber A., Fisher R., Müller H., 2014. LifeCLEF 2014: Multimedia Life Species Identification Challenges. In: E. Kanoulas, M. Lupu, P. Clough, M. Sanderson, M. Hall, A. Hanbury and E. Toms. Information Access Evaluation. Multilinguality, Multimodality, and Interaction. Berlin: Springer International Publishing, 229-249. (Lecture Notes in Computer Science; 8685). [Editor link]
  • Goëau, H., Bonnet, P., Joly, A., Affouard, A., Bakic, V., Barbe, J., Dufour-Kowalski, S., Selmi, S., Yahiaoui, I., Vignau, C., Barthélémy, D., Boujemaa, N., 2014. Pl@ntNet mobile 2014: Android port and new features. In Kankanhalli, M., Rueger, S., Manmatha, R. (Eds) ICMR 2014 - Proceedings of the ACM International Conference on Multimedia Retrieval . New York : ACM Press, 527-258 p. [Editor link]

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