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, Saudi Arabia (4) Department Life and Environmental Sciences

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, Biology Department, Albion College, Albion MI 49224 USA * corresponding author Email: romain.david@imbe.fr Acknowledgements: This manuscript is a result of DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) project, funded by the European Union under the 7th Framework Program, 'The Ocean of Tomorrow' Theme (grant agreement no. 308392), www.devotes-project.eu. Maria C. Uyarra was partially funded through the Spanish program for Talent and Employability in R+D+I This work is a contribution to the Labex

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M. Al-rshaidat, A. Snider, S. Rosebraugh, A. Devine, T. Devine et al., Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea, Genome, vol.26, issue.1, pp.724-737, 2016.
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L. González-goñi, A. Borja, and M. C. Uyarra, Comparación de herramientas de análisis de imagen: eficiencia y uso en ecología bentónica de sustrato duro, Rev Investig Mar, vol.24, pp.1-12, 2017.

M. Sini, S. Kipson, C. Linares, D. Koutsoubas, and J. Garrabou, The Yellow Gorgonian Eunicella cavolini: Demography and Disturbance Levels across the Mediterranean Sea, PLOS ONE, vol.8, issue.5, p.126253, 2015.
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URL : https://hal.archives-ouvertes.fr/hal-01212696

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C. K. , G. R. Somerfield, P. J. Warwick, and R. M. , Change in marine communities: an approach to statistical analysis and interpretation, 2014.

K. R. Clarke and R. N. Gorley, , 2015.

R. Core and D. Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing

M. Spalding, H. Fox, G. Allen, N. Davidson, Z. Ferdaña et al., Marine Ecoregions of the World: A Bioregionalization of Coastal and Shelf Areas, BioScience, vol.92, issue.7, pp.573-583, 2007.
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C. Mellin, D. Mouillot, M. Kulbicki, T. Mcclanahan, L. Vigliola et al., Humans and seasonal climate variability threaten large-bodied coral reef fish with small ranges, Nature Communications, vol.8, 2016.
DOI : 10.1002/sim.1545

URL : https://hal.archives-ouvertes.fr/hal-01282870

N. Van-hoytema, V. Bednarz, U. Cardini, M. Naumann, F. Horani et al., The influence of seasonality on benthic primary production in a Red Sea coral reef, Marine Biology, vol.32, issue.3, p.52, 2016.
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C. Pennesi and R. Danovaro, Assessing marine environmental status through microphytobenthos assemblages colonizing the Autonomous Reef Monitoring Structures (ARMS) and their potential in coastal marine restoration, Marine Pollution Bulletin, vol.125, issue.1-2, 2017.
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K. Hayes, R. Cannon, K. Neil, and G. Inglis, Sensitivity and cost considerations for the detection and eradication of marine pests in ports, Marine Pollution Bulletin, vol.50, issue.8, pp.823-834, 2005.
DOI : 10.1016/j.marpolbul.2005.02.032

L. Carugati, C. Corinaldesi, A. Dell-'anno, and R. Danovaro, Metagenetic tools for the census of marine meiofaunal biodiversity: An overview, Marine Genomics, vol.24, 2015.
DOI : 10.1016/j.margen.2015.04.010

J. Pearman, X. Irigoien, and S. Carvalho, Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea, Marine Genomics, vol.26, pp.29-39, 2016.
DOI : 10.1016/j.margen.2015.10.008

T. L. Zimmerman and J. W. Martin, Artificial Reef Matrix Structures (Arms): An Inexpensive and Effective Method for Collecting Coral Reef-Associated Invertebrates, Gulf and Caribbean Research, vol.16, issue.1, pp.59-64, 2004.
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, Annexe 7 : Activité scientifique en support ou en complément du travail de thèse Articles dans une revue

R. David, M. C. Uyarra, and S. Carvalho,

R. Cahill, L. Danovaro, A. Carugati, J. De-jode, D. Féral et al., Photo analyses of Autonomous Reef Monitoring Structures, as monitoring tools to detect spatial, environmental and anthropic pressure effects, Marine Pollution Bulletin, 2018.

R. David, A. C. Nabeiro, J. Féral, and A. Delavaud,

R. Bourqui, V. Breton, D. Couvet, A. Dias, S. Gachet et al.,

M. Leydet, G. Loïs, V. M. Muñoz, J. Meunier, I. Mougenot et al.,

A. Specht, C. Surace, and T. Tatoni, Bilan des journées du GRAAL 2016 et avenir de l'utilisation des graphes en écologie, Nature, 2018.

A. De-jode, R. David, A. Haguenauer, A. E. Cahill, Z. Erga et al., Multiple cryptic species, spatial and ecological differentiation in a major builder of coralligenous habitats, 2018.

L. Thierry-de-ville, D. Avray, and D. Ami,

. Féral, Application of the Ecosystem Service Concept to a Local-Scale: The Cases of Coralligenous Habitats in the North-Western Mediterranean Sea. 2017 accepted. Marine Pollution Bulletin, p.1624589

A. E. Cahill, J. Pearman, A. Borja, L. Carugati, S. Carvalho et al., A comparative analysis of metabarcoding and morphology-based identification of benthic communities across different regional seas, Ecology and Evolution, vol.3, 2018.
DOI : 10.1111/j.2041-210X.2012.00198.x

URL : https://hal.archives-ouvertes.fr/hal-01886882

A. E. Cahill, A. De-jode, S. Dubois, Z. Bouzaza, D. Aurelle et al., Anne Chenuil, (online pas encore pagine 2017) A multispecies approach reveals hot-spots and cold-spots of diversity and connectivity in species with contrasting dispersal modes, Molecular Ecology, issue.23, pp.266563-6577, 2017.

R. David, L. Bernard, C. Blanpain, A. Dias, J. Féral et al., Visualisation de données sous forme de graphes en archéologie. Rencontre opérationnelle des archéologues d'ArkeoGIS et des écologuesd'IndexMed . Digital Archaeology, iste open science, pp.17-18

, Operational-meeting?. ?hal-01617580?

S. Sartoretto, T. Schohn, C. Bianchi, C. Morri, and J. Garrabou,

R. David, J. Féral, and G. Gatti, An integrated method to evaluate and monitor the conservation state of coralligenous habitats: The INDEX-COR approach, Marine Pollution Bulletin, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01541141

V. Gerovasileiou, T. Dailianis, and E. Panteri,

M. Gatti and . Sini,

A. Do?an, L. Thierry-de-ville, D. Avray, R. David, E. ?inar et al., CIGESMED for divers: Establishing a citizen science initiative for the mapping and monitoring of coralligenous assemblages in the Mediterranean Sea, Biodiversity Data Journal, Pensoft, issue.e8692, p.54, 2016.

R. Danovaro, L. Carugati, B. Marco, A. E. Cahill, S. D. et al.,

M. Wilson, S. Lo-martire, and . Greco,

, Implementing and Innovating Marine Monitoring Approaches for Assessing Marine Environmental Status.. Frontiers in Marine Science, Frontiers Media, 2016.

A. Víctor-méndez-muñoz, R. Cohen-nabeiro, and . David,

. Tatoni, Analysis on the Graph Techniques for Data-mining and Visualization of Heterogeneous Biodiversity Data Sets, Proceedings of the 2nd International Conference on Complexity, Future Information Systems and Risk, pp.144-151, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01541140

B. Madon, R. David, R. Garello, L. Pendleton, and R. Fablet,

, Alert: Towards Real-time, High Resolution Navigational Software for Whale Avoidance

, SUSTECH 2017 : 5th annual IEEE Conference on Technologies for Sustainability, 2017.

R. David, J. Féral, and T. Tatoni, Architecture, concepts et services d'un système d'indexation de données distribuées pour l'observation à large échelle en écologie marine, 32ème Conférence sur la Gestion de Données -Principes, Technologies et Applications, 2016.

R. David and J. Féral,

V. Breton, A. De-jode, A. Delavaud, A. Dias, S. Gachet et al., IndexMed projects: new tools using the CIGESMED DataBase on Coralligenous for indexing, visualizing and data mining based on graphs
URL : https://hal.archives-ouvertes.fr/hal-01425559

S. Sauvage, 8th International Congress on Environmental Modelling and Software International Environmental Modelling and Software Society (iEMSs) 8th International Congress on Environmental Modelling and Software, 2016.

F. Toulouse and S. Sauvage, http://www.iemss.org/society/index.php/iemss-2016-proceedings, 8th, International Congress on Environmental Modelling and Soft ware, p.32, 2016.

C. ,

R. David, J. Féral, S. Gachet, A. Dias, C. Blanpain et al., A First Prototype for Indexing, Visualizing and Mining Heterogeneous Data in Mediterranean Ecology: Within the IndexMed Consortium Interdisciplinary Framework, 2015 11th International Conference on Signal-Image Technology & Internet-Based Systems (SITIS), pp.232-239, 2015.
DOI : 10.1109/SITIS.2015.119

URL : https://hal.archives-ouvertes.fr/hal-01433600

K. Sevastou, N. Papadopoulou, C. Smith, H. Teixeira, H. et al.,

S. Cochrane, Defining keystone species in European regional seas: what are the candidates for the Mediterranean? In: 11th Panhellenic Symposium on Oceanography & Fisheries «Aquatic Horizons: Challenges & Perspectives, 2015.

. Greece, Athens: H.C.M.R, pp.13-17, 2015.

J. Féral and C. Arvanitidis,

E. Egea and S. Sartoretto, CIGESMED: Coralligenous based indicators to evaluate and monitor the "good environmental statut of the Mediterranean coastal waters, a SeasEra project, 2nd Mediterranean Symposium on the conservation of Coralligenous & other Calcareous Bio-Concretions Proceedings of the 2nd, 2014.

, Mediterranean Symposium on the conservation of Coralligenous & other Calcareous Bio-Concretions

S. Sartoretto, R. David, D. Aurelle, A. Chenuil-maurel, D. Guillemain et al., 2014) -An integrated approach to evaluate and monitor the conservation state of coralligenous bottoms: the INDEX-COR method

, Proceeding of the 2nd Mediterranean Symposium on the conservation of Coralligenous & other Calcareous Bio-Concretions, 2014.

R. David, C. Arvanitidis, M. Ertan-Çinar, S. Sartoretto, and . Doan,

A. Chenuil-maurel and J. Féral, -CIGESMED habitat's characterization: a simple and reusable typology at the Mediterranean scale, 2nd Mediterranean Symposium on the conservation of Coralligenous & other Calcareous Bio-Concretions Proceedings of the 2nd Mediterranean Symposium on the conservation of Coralligenous & other Calcareous Bio-Concretions, 2014.

R. David, C. Arvanitidis, M. Ertan-Çinar, S. Sartoretto, S. Dubois et al., Anne Chenuil-Maurel, Jean-Pierre Féral, (2014) -CIGESMED Protocols : how to implement a multidisciplinary approach on a large scale for coralligenous habitats surveys

, Mediterranean Symp. on the Conservation of coralligenous and other calcareous bioconcretions , Portoro?, Slovenia, pp.29-30, 2014.

R. David, S. Dubois, Z. Erga, D. Guillemain, L. Thierry-de-ville et al., Anne Chenuil-Maurel, Jean-Pierre Féral, (2014) -CIGESMED.'s protocol and network (Coralligenous basEd. Indicators to evaluate and monitor the " Good Environmental Status " of Mediterranean coastal waters), Proceedings of the 5th International Symposium of Monitoring of Mediterranean coastal areas: problems and measurement techniques, pp.828-843, 2014.

, Chapitres d'ouvrage

R. David, J. Féral, and C. Blanpain, -Ecological Data Preservation in the context of IndexMed, p.pp, 2015.

R. David, S. Dubois, Z. Erga, D. Guillemain, L. Thierry-de-ville-d-'avray et al., Frédéric Zuberer, Anne Chenuil, Jean-Pierre Féral with other contributors (2015) - " CIGESMED*'s protocol and network (Coralligenous based Indicators to Evaluate and Monitor the « good ecological status, of the MEDiterranean coastal waters) " , CIGESMED Project. Pages 828-843

. Florence, ISBN : 978-88-95597-19-5 (Fifth Symposium Monitoring of Mediterranean coastal areas : problems and measurement techniques Livorno (Italy), pp.17-19, 2014.

J. Féral and R. David, 22. Zones c??ti??res et d??veloppement durable??: une ??quation ?? r??soudre, CNRS Editions, vol.2013, pp.96-97
DOI : 10.4000/books.editionscnrs.10647

, Alison Specht, remotely Developing crediting/rewarding mechanisms to foster resources (data and materials) sharing in Research: towards recommendations -Case study : the biodiversity community " IG Sharing Rewards and Credit (SHARC) -RDA 11th Plenary meeting, 2018.

, Octobre, vol.2017

S. Archambeau, D. Auber, and N. Bailly,

C. Blanpain, V. Breton, A. Chenuil-maurel, A. Cohen-nabeiro, A. Dias et al.,

A. Michollet, C. Specht, J. Surace, T. Raynal, J. David et al., ontology-semantic-web-for-biodiversity- ecosystem-research-programme ? 9 Anne Chenuil-Maurel, Prérequis, principes et bonnes pratiques driihm2017 : Séminaire annuel du LabEx DRIIHM 2017, pp.11-14, 2017.

R. David, J. Féral, A. Archambeau, D. Auber, N. Bailly et al., Results of IndexMed GRAIL Days 2016: How to use standards to build GRAphs and mIne data for environmental research " TDWG 2016 annual conference Learn about Open Access, open data, data papers, data sensibility and property and the debate around it and why, Décembre, vol.2016

R. David, J. Féral, N. Bailly, V. Cyrille-blanpain, D. Breton et al., Graph approach of heterogeneous data, the new possibilities developed by the IndexMed consortium for data mining in Mediterranean ecology, Sciences - Kristineberg, pp.24-28

B. Ledoux, B. Mérigot, A. Weber, and A. Chenuil, Etats- Unis) http://www.sicb.org/meetings, Coralligenous habitats assessment in SW Greece: the case of Korinthiakos Gulf, pp.7-11, 2016.

, Charalampos Dimitriadis, Nikitas Michalakis, Alper Do?an Establishing a citizen science initiative for the mapping and monitoring of coralligenous assemblages in the Mediterranean Sea, ICZEGAR congress, 2015.

J. Féral, C. Arvanitidis, A. Chenuil-maurel, M. Ertan-Çinar, R. David et al., CIGESMED: Coralligenous based indicators to evaluate and monitor the "good environmental statut" of the Mediterranean coastal waters, a SeasEra project, CIGESMED second general assembly (GA2)

, Ecosystem services provided by coralligenous habitats -Measurement & valuation, CIGESMED second general assembly (GA2), 2015.

G. Mytilène,

E. Panteri, S. Faulwetter, C. Arvanitidis, T. Dailianis, G. Chatzigeorgiou et al., crowd sourcing initiatives in the mediterranean bassin " Presentation at the Biodiversity Information Standards (TDWD) Conference 2014, pp.27-31, 2014.

R. David, J. Féral, A. Archambeau, F. Arnaud, D. Auber et al., Régine Vignes Lebbe, et la communauté IndexM(e)ed, " Indexing and Mining Ecological and Environmental Data : Architecture, concepts et services d'un système d'indexation de données distribuées pour l'observation et l'inter-opération de données à large échelle en écologie / environnement, Séminaire INSIDE "le numérique au service de l'eau, pp.28-29

F. R. De-la, IndexMEED Consortium : Indexing and Mining Ecological and Environmental Data, Comité d'Appuis Scientifique et Technique (CAST), Février, vol.2017, 2016.

, concepts et services d'un système d'indexation de données distribuées pour l'observation à large échelle en écologie marine, 32ème Conférence sur la Gestion de Données -Principes, Technologies et Applications

R. David, J. Féral, A. Archambeau, N. Bailly, C. Blanpain et al., Results of IndexMed GRAIL Days 2016: How to use standards to build GRAphs and mIne data for environmentaL research?" Séminaire GBIF EUBON IDIV "Symposium on the Mobilization of Structured Biodiversity DataResults of IndexMed GRAIL Days 2016: How to use standards to build GRAphs and mIne data for environmentaL research, LifeWatch and EUDAT workshop : Ontology & Semantic Web for Research, pp.11-13

R. David, J. Féral, A. Archambeau, D. Auber, N. Bailly et al., Results of IndexMed GRAIL Days 2016: How to use standards to build GRAphs and mIne data for environmentaL research?" RDA 9th Plenary meeting poster session https://www.rd-alliance.org/plenaries/rda-ninth-plenary-meeting-barcelona/rda-9th- plenary-poster-session ? 9 ? 10 févr, Results of IndexMed GRAIL Days 2016: How to use standards to build, 2017.

A. Chenuil, Strong genetic structure in Lithophyllum cabiochiae/stictaeforme around Marseilles. Local adaptation, niche differentiation or just lack of connectivity? Annual conference of French Phycology Society, 2014.

L. Thierry-de-ville, D. , D. Ami, A. Chenuil, and R. David, Jean-Pierre Féral : with contributors, How food security can be linked to the ecological and economic status of the coralligenous habitats of the Mediterranean Sea? Biodiversity and Food Security ? From Trade-offs to Synergies, 2014.

R. David, C. Arvanitidis, M. Ertan-Çinar, S. Sartoretto, S. Doan et al., Laure Thierry de Ville d'Avray, Frederic Zuberer, Anne Chenuil-Maurel, Jean-Pierre Féral, « CIGESMED habitat's characterization : a simple and reusable typology at the Mediterranean scale » 2ème Symposium CAR ASP : The 2nd Mediterranean symposium on Coralligenous and other calcareous bio-concretions, Portoroz, pp.29-30

J. Melih-ertan-Çinar, C. Féral, R. Arvanitidis, E. David, T. Taskin et al., Preliminary assessment of macrobenthic coralligenous assemblages across the Mediterranean sea " 2ème Symposium CAR ASP : The 2nd Mediterranean symposium on Coralligenous and other calcareous bio-concretions, pp.29-30, 2014.

, Study of the genetic diversity of the rhodophyte Lithophyllum stictaeforme/cabiochiae in the North Ouest Mediterranean. 7 th Helecos congress, pp.9-12, 2014.

R. David, S. Dubois, Z. Erga, D. Guillemain, L. Thierry-de-ville et al., CIGESMED* or how to integrate combined scientific and amateur large sets of heterogeneous data on coralligenous habitats for the effective evaluation of the "Good Environmental Status, Fifth Symposium Monitoring of Mediterranean coastal areas: problems and measurement techniques, 2014.

J. Féral, C. Arvanitidis, A. Chenuil, M. Ertan-Çinar, R. David et al., CIGESMED : Coralligenous based Indicators to evaluate and monitor the « Good Environmental Status » of the Mediterranean coastal waters. SeasEra project Towards Integrated Marine Research Strategy and Programmes, pp.3848-01448881, 2016.

?. Smith, N. Papadopoulou, K. Sevastou, A. Franco, H. Teixeira et al., Report on identification of keystone species and processes, p.105, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01790558

, pp + 1 Annex

, Stages co-encadrés avec J.P. Féral pendant la thèse, 2015.

?. Dubar, Mise en oeuvre d'un protocole pour l'étude de la composition taxonomique des habitats coralligènes en fonction de la luminosité, p.pp, 2015.

W. El and G. , Qualification de données de CIGESMED : Un système de prospection de données pour l'aide à la gestion des habitats coralligènes, 2014.

?. Dorian-guillemain, Etude de la variabilité de la structure des peuplements coralligènes sur des îlots marseillais à profondeur constante dans le cadre du programme européen SeasEra CIGESMED, 2014.

?. Laure-thierry-de-ville-d-'avray, Etude de la variabilité de la composition observée d'habitats coralligènes liée à l'application d'un protocole d'observation au moyen de quadra-photos. Mémoire de fin d'étude, master d'océanographie, spécialité biologie et écologie marine, 2014.

, Sommaire 1) Enjeux et principes de la curation de données 2) Avant : la mise en place du protocole de curation de données 3) Pendant : l'application du protocole de curation de données en vue d'une représentation sous forme de graphes

. Après, curation de données Dans le domaine de l'environnement, la fréquence des campagnes de collecte de données (missions de terrain, capteurs optiques ou radar, suivi de la qualité des eaux, recensement automatique ou semi-automatique des taxons, etc.) permettent d'acquérir un volume considérable de données. A cause de leur hétérogénéité, celles-ci sont néanmoins difficiles à agréger pour avoir

, Améliorer l'interopérabilité nécessite de s'appuyer sur la curation de ces données avec une sémantique commune

, Pour curer un jeu de données, il faut aller plus loin que le " nettoyage " de ses imperfections

. La-curation-de-données and . Du-latin-curare-qui-signifie, prendre soin " , est essentielle avant tout processus d'analyse ; elle consiste à améliorer la capacité des données à décrire un système de manière univoque et explicite. Elle est essentielle pour préparer un jeu de données pour chaque nouveau type d'analyse ou agréger différents jeux de données d'origines, de structures et de formats différents. La curation permet notamment de construire des graphes

. Rappel, points que l'on appelle des noeuds (sommets en mathématique ou objets en informatique) reliés par des traits (segments) ou flèches nommées arêtes (ou bien liens, arcs ou attributs). L'ensemble des arêtes entre les noeuds forme une figure similaire à un réseau. La représentation de données sous forme de graphes permet de relier des objets (champs/entités de la base de données ou valeurs de ces champs

, il faut choisir dans la base de données les " objets " (c'està-dire le ou les champs de la base de données) qui vont servir de " noeuds " / " sommets " aussi appelé " entités " , et les champs descripteurs (que l'on appelle attributs) des objets choisis pour en faire des liens/arêtes aussi appelés, Visualisation sous forme de graphes de données en écologie et environnement : retour sur les ateliers 2017

, Janvier, 2018.

, Consortium IndexMEED, vol.365

, CONTRIBUTEURS

M. Aux-experts-qui-ont-répondu-présent, Alrick Dias (OSU Institut Pythéas), Baptiste Laporte (FRB), Julien Lecubin (OSU Institut Pythéas)

, Atelier préparatoire à la visualisation » et à l'atelier « Visualisation de données, Merci aux participants aux deux ateliers « Curation de données Eloïse Trigodet (MNHN)

R. Animateur-du and . David, IMBE-CNRS

, IMBE-CNRS) et Aurélie Delavaud (FRB)

. Début-de-la-mission, , 2017.

, Fin de la mission : Novembre, 2017.

G. Le, . Madics, C. Aix-marseille-merci-aux, . Ecoscope, . Frb et al., Ont participé, et GDR MaDICS pour leur soutien humain et financier à l'organisation des ateliers et manifestations de, 2016.

, Remerciements

M. and D. Parade, Scénario Interactif) pour son appui technique à l'utilisation du logiciel Gephi, merci à Robin Goffaux (FRB) et Samir Hamdi-Cherif (FRB) pour leur aide à la curation de données sur Excel, merci à Romain David (IMBE) pour son aide à la réalisation des étapes de curation, J. Lecubin)

, Citation

, Consortium IndexMEED Visualisation sous forme de graphes de données en écologie et environnement : retour sur les ateliers 2017, 2017.

, Présentation de l'étude

. Dans-le-domaine-de-l-'écologie-et-de-la-biodiversité, augmentation des fréquences et volumes d'acquisition de données (observations de terrain, capteurs optiques, capteurs radar, télédétection, systèmes de suivi de la qualité des eaux, recensement automatique ou semi-automatique des taxons, séquençage, génotypage, etc..) a abouti à une accumulation considérable de données hétérogènes et dispersées qu

, Illustration 4 : Représentation des deux groupes d'entités obtenus après application d'un algorithme de classification hiérarchique

, Les informations des deux groupes de données ont été exportées et des analyses complémentaires doivent être menées pour tenter de révéler ce qui différencie les deux groupes de jardins

, Problématique 3 : Géo-Spatialiser les données

, Une seconde approche avec utilisation des coordonnées GPS est ensuite choisie. Le " Layout GEM (Frick) " est appliqué pour représenter les données avec une notion de distance entre les noeuds. Un panneau de visualisation " Geographic view " est utilisé, et l'algorithme Betweenness centrality et la représentation par dégradé de couleur via la méthode d'alpha mapping sont appliqués

, Aurillac, Metz et Le Mans et représentent donc des villes par lesquelles passent les maximums de " chemins " . Aurillac semblerait donc être une ville " charnière