Gestion d'échantillons pour la recherche scientifique avec Collec-Science

Les acteurs des laboratoires de recherche scientifique environnementale collectent regulierement de nombreux echantillons qui sont ensuite analyses et stockes. Leur gestion sur le long terme s'inscrit dans une strategie qu'il s'agit de definir puis de mettre en oeuvre via des outils informatiques adaptes. Cet article presente cette strategie, puis sa declinaison dans un systeme d'information developpe sous le nom de Collec-Science, offrant un support adequat pour la tracabilite, la diversite des donnees a traiter et l'autonomie des utilisateurs. Il presente egalement les perspectives de ces travaux en matiere d'animation de communaute scientifique, a la fois sur les plans organisationnels et operationnels, dans le contexte d'une science ouverte.

[1]  Heimo Müller,et al.  From the evaluation of existing solutions to an all-inclusive package for biobanks , 2017, Health and Technology.

[2]  Markus List,et al.  Efficient Sample Tracking With OpenLabFramework , 2014, Scientific reports.

[3]  Karlis Podnieks,et al.  A System for Information Management in BioMedical Studies—SIMBioMS , 2009, Bioinform..

[4]  Gregory Butler,et al.  The EnzymeTracker: an open-source laboratory information management system for sample tracking , 2011, BMC Bioinformatics.

[5]  Ibón Cancio Uriarte,et al.  The Nagoya protocol , 2018 .

[6]  Prakash M. Nadkarni,et al.  Guidelines for the effective use of entity-attribute-value modeling for biomedical databases , 2007, Int. J. Medical Informatics.

[7]  H. Drouineau,et al.  Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect? , 2012 .

[8]  Alan Christoffels,et al.  Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking , 2017, Biopreservation and biobanking.

[9]  J. Lobry,et al.  Structure of the Gironde estuarine fish assemblages: a comparison of European estuaries perspective , 2003 .

[10]  Erik Schultes,et al.  The FAIR Guiding Principles for scientific data management and stewardship , 2016, Scientific Data.

[11]  Vincent Bretagnolle,et al.  Towards better traceability of field sampling data , 2017, Comput. Geosci..

[12]  Randall T. Schuh,et al.  Integrating specimen databases and revisionary systematics , 2012, ZooKeys.

[13]  Benedikt Fecher,et al.  Open Science: One Term, Five Schools of Thought , 2013 .

[14]  Simon J. D. Cox,et al.  Ontology for observations and sampling features, with alignments to existing models , 2016, Semantic Web.

[15]  Suzanne A. Pierce,et al.  Toward the Geoscience Paper of the Future: Best practices for documenting and sharing research from data to software to provenance , 2016 .

[16]  P. Elie,et al.  Tracking continental habitat shifts of eels using otolith Sr/Ca ratios: validation and application to the coastal, estuarine and riverine eels of the Gironde-Garonne-Dordogne watershed , 2005 .

[17]  Katherine C Sexton,et al.  Development of the ISBER Best Practices for Repositories: Collection, Storage, Retrieval and Distribution of Biological Materials for Research. , 2012, Biopreservation and biobanking.

[18]  B. Sautour,et al.  Abrupt shifts in the Gironde fish community: an indicator of ecological changes in an estuarine ecosystem , 2016 .

[19]  Vicki A. Funk,et al.  Utility of QR codes in biological collections , 2013, PhytoKeys.

[20]  Brooks Hanson,et al.  Liberating field science samples and data , 2016, Science.