IndexMEED cases studies using "Omics" data with graph theory
Romain David
(1)
,
Jean-Pierre Féral
(1)
,
Sophie Archambeau
(2)
,
Fanny Arnaud
(3)
,
David Auber
(4)
,
Nicolas Bailly
(5)
,
Loup Bernard
(6)
,
Laure Berti-Équille
(7)
,
Cyrille Blanpain
(8)
,
Vincent Breton
(9)
,
Anne Chenuil-Maurel
(1)
,
Anna Cohen Nabeiro
(10)
,
Alrick Dias
(1)
,
Aurélie Delavaud
(10)
,
Robin Goffaud
(10)
,
Sophie Gachet
(1)
,
Karina Gibert
(11)
,
Manuel Herrera Fernandez
(12)
,
Luc Hogie
(13)
,
Dino Ienco
(14)
,
Romain Julliard
(15)
,
Yvan Le Bras
(15)
,
Julien Lecubin
(8)
,
Yannick Legre
(9)
,
Michelle Leydet
(1)
,
Grégoire Lois
(15)
,
Bénédicte Madon
(16)
,
François Marchal
(17)
,
Víctor Méndez Muñoz
(18)
,
Jean-Charles Meunier
(19)
,
Jean-Baptiste Mihoub
(15)
,
Isabelle Mougenot
(20)
,
Sophie Pamerlon
(19)
,
Eric Peletier
(21)
,
Geneviève Romier
(9)
,
Dad Roux-Michollet
(22)
,
Alison Specht
(10)
,
Christian Surace
(19)
,
Jean-Claude Raynal
(23)
,
Thierry Tatoni
(1)
1
IMBE -
Institut méditerranéen de biodiversité et d'écologie marine et continentale
2 GBIF France - Global Biodiversity Information Facility France
3 EVS - Environnement, Ville, Société
4 LaBRI - Laboratoire Bordelais de Recherche en Informatique
5 HCMR - Hellenic Centre for Marine Research
6 ARCHIMEDE - Archéologie et histoire ancienne : Méditerranée - Europe
7 IRD - Institut de Recherche pour le Développement
8 OSU PYTHEAS - Institut Pythéas
9 Institut des Grilles et du Cloud
10 FRB - Fondation pour la recherche sur la Biodiversité
11 UPC - Universitat Politècnica de Catalunya = Université polytechnique de Catalogne [Barcelona]
12 University of Bath [Bath]
13 KAIROS - Logical Time for Formal Embedded System Design
14 ADVANSE - ADVanced Analytics for data SciencE
15 CESCO - Centre d'Ecologie et des Sciences de la COnservation
16 IUEM - Institut Universitaire Européen de la Mer
17 ADES - Anthropologie bio-culturelle, Droit, Ethique et Santé
18 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
19 LAM - Laboratoire d'Astrophysique de Marseille
20 UMR 228 Espace-Dev, Espace pour le développement
21 IG - Institut de Génomique d'Evry
22 GRAIE - Groupe de Recherche Rhône Alpes sur les Infrastructures et l'Eau
23 ECCOREV - Ecosystèmes continentaux et risques environnementaux
2 GBIF France - Global Biodiversity Information Facility France
3 EVS - Environnement, Ville, Société
4 LaBRI - Laboratoire Bordelais de Recherche en Informatique
5 HCMR - Hellenic Centre for Marine Research
6 ARCHIMEDE - Archéologie et histoire ancienne : Méditerranée - Europe
7 IRD - Institut de Recherche pour le Développement
8 OSU PYTHEAS - Institut Pythéas
9 Institut des Grilles et du Cloud
10 FRB - Fondation pour la recherche sur la Biodiversité
11 UPC - Universitat Politècnica de Catalunya = Université polytechnique de Catalogne [Barcelona]
12 University of Bath [Bath]
13 KAIROS - Logical Time for Formal Embedded System Design
14 ADVANSE - ADVanced Analytics for data SciencE
15 CESCO - Centre d'Ecologie et des Sciences de la COnservation
16 IUEM - Institut Universitaire Européen de la Mer
17 ADES - Anthropologie bio-culturelle, Droit, Ethique et Santé
18 UAB - Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
19 LAM - Laboratoire d'Astrophysique de Marseille
20 UMR 228 Espace-Dev, Espace pour le développement
21 IG - Institut de Génomique d'Evry
22 GRAIE - Groupe de Recherche Rhône Alpes sur les Infrastructures et l'Eau
23 ECCOREV - Ecosystèmes continentaux et risques environnementaux
Romain David
- Fonction : Auteur
- PersonId : 11404
- IdHAL : romain-david
- ORCID : 0000-0003-4073-7456
- IdRef : 233679359
Jean-Pierre Féral
- Fonction : Auteur
- PersonId : 10344
- IdHAL : jean-pierre-feral
- ORCID : 0000-0001-7627-0160
- IdRef : 070528799
Fanny Arnaud
- Fonction : Auteur
- PersonId : 7085
- IdHAL : fanny-arnaud
- ORCID : 0000-0002-8784-1384
- IdRef : 178365378
David Auber
- Fonction : Auteur
- PersonId : 13587
- IdHAL : david-auber
- ORCID : 0000-0002-1114-8612
- IdRef : 069771332
Loup Bernard
- Fonction : Auteur
- PersonId : 1224996
- ORCID : 0000-0003-3320-8046
- IdRef : 076131904
Laure Berti-Équille
- Fonction : Auteur
- PersonId : 19540
- IdHAL : laure-berti-equille
- ORCID : 0000-0002-8046-0570
- IdRef : 130675725
Anne Chenuil-Maurel
- Fonction : Auteur
- PersonId : 15766
- IdHAL : anne-chenuil
- ORCID : 0000-0001-8141-7147
- IdRef : 133649393
Alrick Dias
- Fonction : Auteur
- PersonId : 1336772
- IdHAL : alrick-dias
- ORCID : 0000-0002-2088-278X
Aurélie Delavaud
- Fonction : Auteur
- PersonId : 997170
Sophie Gachet
- Fonction : Auteur
- PersonId : 12349
- IdHAL : sophie-gachet
- ORCID : 0000-0002-3599-5189
- IdRef : 070970858
Luc Hogie
- Fonction : Auteur
- PersonId : 1334712
- IdHAL : lhogie
- ORCID : 0000-0001-8044-5672
Dino Ienco
- Fonction : Auteur
- PersonId : 6226
- IdHAL : dino-ienco
- ORCID : 0000-0002-8736-3132
- IdRef : 172688183
Romain Julliard
- Fonction : Auteur
- PersonId : 1238108
- ORCID : 0000-0001-8897-2514
- IdRef : 135542812
Yvan Le Bras
- Fonction : Auteur
- PersonId : 184303
- IdHAL : yvan-le-bras
- ORCID : 0000-0002-8504-068X
- IdRef : 150878001
Michelle Leydet
- Fonction : Auteur
- PersonId : 20728
- IdHAL : michelle-leydet
- ORCID : 0000-0003-1123-3427
- IdRef : 253120101
François Marchal
- Fonction : Auteur
- PersonId : 21511
- IdHAL : francois-marchal
- ORCID : 0000-0001-7479-2360
Jean-Charles Meunier
- Fonction : Auteur
- PersonId : 1362957
- IdRef : 27631655X
Jean-Baptiste Mihoub
- Fonction : Auteur
- PersonId : 174212
- IdHAL : jb-mihoub
- ORCID : 0000-0002-5354-850X
- IdRef : 144503220
Isabelle Mougenot
- Fonction : Auteur
- PersonId : 14914
- IdHAL : isabelle-mougenot
- ORCID : 0000-0002-1287-3269
- IdRef : 16790714X
Geneviève Romier
- Fonction : Auteur
- PersonId : 174586
- IdHAL : genevieve-romier
Dad Roux-Michollet
- Fonction : Auteur
- PersonId : 880469
Alison Specht
- Fonction : Auteur
- PersonId : 784314
- ORCID : 0000-0002-2623-0854
Christian Surace
- Fonction : Auteur
- PersonId : 11510
- IdHAL : christian-surace
- ORCID : 0000-0003-2592-0113
Thierry Tatoni
- Fonction : Auteur
- PersonId : 173998
- IdHAL : thierry-tatoni
- ORCID : 0000-0002-2557-4444
- IdRef : 069886679
Résumé
Data produced within marine and terrestrial biodiversity research projects that evaluate and monitor Good Environmental Status, have a high potential for use by stakeholders involved in environmental management. However, environmental data, especially in ecology, are not readily accessible to various users. The specific scientific goals and the logics of project organization and information gathering lead to a decentralized data distribution. In such a heterogeneous system across different organizations and data formats, it is difficult to efficiently harmonize the outputs. Few tools are available to assist. For instance standards and specific protocols can be applied to interconnect databases. Such semantic approaches greatly increase data interoperability.
This communication present the recent results and the consortium IndexMEED (Indexing for Mining Ecological and Environmental Data) activity that aims to build new approaches to investigate complex research questions, and support the emergence of new scientific hypotheses based on graph theory Auber et al. 2014). Current developments in data mining based on graphs, as well as the potential for relevant contributions to environmental research, particularly about strategic decision-making, and new ways of organizing data will be presented (David et al. 2015). In particular, the consortium makes decisions on how i) to analyze heterogeneous distributed data spread throughout different databases combining molecular and habitat characteristics data [3], ii) to create matches and incorporate some approximations, iii) to identify statistical relationships between observed data and the emergence of contextual patterns using a calculation library and distributed calculation center at the European level, iv) to encourage openness and sharing data while complying with the general principles of FAIR (Findable, Accessible, Interoperable, Re-usable and citable) in order to enhance data value and their utilization. IndexMEED participants are now exploring the ability of two scientific communities (ecology sensu lato and computer sciences) to work together, using several studies cases. The ECOSCOPE project aims to meet the need to access structured and complementary omics-datasets to better understand biodiversity state and its dynamics. Indeed, the ECOSCOPE case study targets to visualize, through the graph approach, links between datasets and databases from genetics to ecosystems. Another case study, displaying anthropology fossils and omics on the same graph, will also be presented. DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) and CIGESMED (Coralligenous based Indicators to evaluate and monitor the "Good Environmental Status" of the MEDiterranean coastal water) European projects, conducted by IMBE, are focused on photo quadrats, cartography and omics data of the marine hard bottom in order to discover context patterns helpful to build decision support system building. Study case “65 Millions d’observateurs” French project is testing AskOmics to provide a graph-based querying interface using RDF (Resource Description Framework) and SPARQL technologies.
Scientific questions can be resolved by the new data mining approaches that offer new ways to investigate heterogeneous environmental data with graph mining (Muñoz et al. 2017). The uses of data from biodiversity research demonstrate the prototype functionalities (David et al. 2016) and introduce new perspectives to analyze environmental and societal responses including decision-making at large scale, both at the information system level and the observing system level than at the observed system level.
Format du dépôt | Fichier |
---|---|
Type de dépôt | Article dans une revue |
Résumé |
en
Data produced within marine and terrestrial biodiversity research projects that evaluate and monitor Good Environmental Status, have a high potential for use by stakeholders involved in environmental management. However, environmental data, especially in ecology, are not readily accessible to various users. The specific scientific goals and the logics of project organization and information gathering lead to a decentralized data distribution. In such a heterogeneous system across different organizations and data formats, it is difficult to efficiently harmonize the outputs. Few tools are available to assist. For instance standards and specific protocols can be applied to interconnect databases. Such semantic approaches greatly increase data interoperability.
This communication present the recent results and the consortium IndexMEED (Indexing for Mining Ecological and Environmental Data) activity that aims to build new approaches to investigate complex research questions, and support the emergence of new scientific hypotheses based on graph theory Auber et al. 2014). Current developments in data mining based on graphs, as well as the potential for relevant contributions to environmental research, particularly about strategic decision-making, and new ways of organizing data will be presented (David et al. 2015). In particular, the consortium makes decisions on how i) to analyze heterogeneous distributed data spread throughout different databases combining molecular and habitat characteristics data [3], ii) to create matches and incorporate some approximations, iii) to identify statistical relationships between observed data and the emergence of contextual patterns using a calculation library and distributed calculation center at the European level, iv) to encourage openness and sharing data while complying with the general principles of FAIR (Findable, Accessible, Interoperable, Re-usable and citable) in order to enhance data value and their utilization. IndexMEED participants are now exploring the ability of two scientific communities (ecology sensu lato and computer sciences) to work together, using several studies cases. The ECOSCOPE project aims to meet the need to access structured and complementary omics-datasets to better understand biodiversity state and its dynamics. Indeed, the ECOSCOPE case study targets to visualize, through the graph approach, links between datasets and databases from genetics to ecosystems. Another case study, displaying anthropology fossils and omics on the same graph, will also be presented. DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing good Environmental Status) and CIGESMED (Coralligenous based Indicators to evaluate and monitor the "Good Environmental Status" of the MEDiterranean coastal water) European projects, conducted by IMBE, are focused on photo quadrats, cartography and omics data of the marine hard bottom in order to discover context patterns helpful to build decision support system building. Study case “65 Millions d’observateurs” French project is testing AskOmics to provide a graph-based querying interface using RDF (Resource Description Framework) and SPARQL technologies.
Scientific questions can be resolved by the new data mining approaches that offer new ways to investigate heterogeneous environmental data with graph mining (Muñoz et al. 2017). The uses of data from biodiversity research demonstrate the prototype functionalities (David et al. 2016) and introduce new perspectives to analyze environmental and societal responses including decision-making at large scale, both at the information system level and the observing system level than at the observed system level.
|
Titre |
en
IndexMEED cases studies using "Omics" data with graph theory
|
Auteur(s) |
Romain David
1
, Jean-Pierre Féral
1
, Sophie Archambeau
2
, Fanny Arnaud
3
, David Auber
4
, Nicolas Bailly
5
, Loup Bernard
6
, Laure Berti-Équille
7
, Cyrille Blanpain
8
, Vincent Breton
9
, Anne Chenuil-Maurel
1
, Anna Cohen Nabeiro
10
, Alrick Dias
1
, Aurélie Delavaud
10
, Robin Goffaud
10
, Sophie Gachet
1
, Karina Gibert
11
, Manuel Herrera Fernandez
12
, Luc Hogie
13
, Dino Ienco
14
, Romain Julliard
15
, Yvan Le Bras
15
, Julien Lecubin
8
, Yannick Legre
9
, Michelle Leydet
1
, Grégoire Lois
15
, Bénédicte Madon
16
, François Marchal
17
, Víctor Méndez Muñoz
18
, Jean-Charles Meunier
19
, Jean-Baptiste Mihoub
15
, Isabelle Mougenot
20
, Sophie Pamerlon
19
, Eric Peletier
21
, Geneviève Romier
9
, Dad Roux-Michollet
22
, Alison Specht
10
, Christian Surace
19
, Jean-Claude Raynal
23
, Thierry Tatoni
1
1
IMBE -
Institut méditerranéen de biodiversité et d'écologie marine et continentale
( 188653 )
- Aix Marseille Université, Campus Etoile, Faculté St-Jérôme case 421 Av. . escadrille Normandie-Niemen 13397 MARSEILLE CEDEX 20
- France
2
GBIF France -
Global Biodiversity Information Facility France
( 477416 )
- MNHN, CP 48, 43 rue Buffon, 75005 Paris
- France
3
EVS -
Environnement, Ville, Société
( 145345 )
- 18 Rue Chevreul
69362 LYON CEDEX 07
UMR 5600
- France
4
LaBRI -
Laboratoire Bordelais de Recherche en Informatique
( 3102 )
- Domaine Universitaire 351, cours de la Libération 33405 Talence Cedex
- France
5
HCMR -
Hellenic Centre for Marine Research
( 18532 )
- P.C. 19013 Anavyssos
Attiki
- Grèce
6
ARCHIMEDE -
Archéologie et histoire ancienne : Méditerranée - Europe
( 259783 )
- MISHA - 5, allée du Gal Rouvillois - CS 50008 - 67083 Strasbourg cedex
- France
7
IRD -
Institut de Recherche pour le Développement
( 67872 )
- Siège
Le Sextant
44, bd de Dunkerque
CS 90009
13572 Marseille cedex 02
- France
8
OSU PYTHEAS -
Institut Pythéas
( 351757 )
- Technopôle de Château-Gombert
38, rue Frédéric Joliot-Curie
13388 MARSEILLE cedex 13
- France
9
Institut des Grilles et du Cloud
( 534304 )
- Campus Universitaire des Cézeaux
4 Avenue Blaise Pascal
TSA 60026 / CS 60026
63178 Aubière Cedex
- France
10
FRB -
Fondation pour la recherche sur la Biodiversité
( 430953 )
- 195, rue Saint-Jacques
75005 Paris
- France
11
UPC -
Universitat Politècnica de Catalunya = Université polytechnique de Catalogne [Barcelona]
( 85878 )
- C./Jordi Girona, 1-3, 08034 Barcelona
- Espagne
12
University of Bath [Bath]
( 60512 )
- laverton Down, Bath, North East Somerset BA2 7AY
- Royaume-Uni
13
KAIROS -
Logical Time for Formal Embedded System Design
( 478607 )
- 2004 route des Lucioles BP 93 06902 Sophia Antipolis
- France
14
ADVANSE -
ADVanced Analytics for data SciencE
( 409262 )
- LIRMM, 161 rue Ada, 34000 Montpellier
- France
15
CESCO -
Centre d'Ecologie et des Sciences de la COnservation
( 237629 )
- 55 rue Buffon - 75005 PARIS
- France
16
IUEM -
Institut Universitaire Européen de la Mer
( 413764 )
- IUEM Technopôle Brest-Iroise - rue Dumont d'Urville - 29280 Plouzané
- France
17
ADES -
Anthropologie bio-culturelle, Droit, Ethique et Santé
( 186857 )
- Faculté de Médecine Secteur Nord 51, Boulevard Pierre Dramard 13344 MARSEILLE CEDEX 15
- France
18
UAB -
Universitat Autònoma de Barcelona = Autonomous University of Barcelona = Universidad Autónoma de Barcelona
( 98227 )
- UAB Campus 08193 Bellaterra Barcelona
- Espagne
19
LAM -
Laboratoire d'Astrophysique de Marseille
( 179944 )
- Pôle de l'Étoile Site de Château-Gombert 38, rue Frédéric Joliot-Curie 13388 Marseille cedex 13
- France
20
UMR 228 Espace-Dev, Espace pour le développement
( 196623 )
- IRD - Maison de la Télédétection - 500 rue Jean-François Breton - 34093 Montpellier
- France
21
IG -
Institut de Génomique d'Evry
( 40508 )
- 2 rue Gaston Crémieux CP5706 91057 EVRY CEDEX
- France
22
GRAIE -
Groupe de Recherche Rhône Alpes sur les Infrastructures et l'Eau
( 516553 )
- Campus LyonTech la Doua
66 bd Niels Bohr – CS 52132
69603 Villeurbanne Cedex
- France
23
ECCOREV -
Ecosystèmes continentaux et risques environnementaux
( 96756 )
- Europôle de l'Arbois
BP 80
13545 Aix-en-Provence cedex 4
- France
|
Numéro |
2
|
Licence |
Paternité
|
Volume |
1
|
Comité de lecture |
Oui
|
Page/Identifiant |
340-361
|
Langue du document |
Anglais
|
Date de publication |
2017
|
Nom de la revue |
|
Audience |
Internationale
|
Vulgarisation |
Non
|
Titre de la collection |
TDWG 2017 - Proceedings
|
Voir aussi |
|
Domaine(s) |
|
Projet(s) ANR |
|
Mots-clés |
en
Thesaurus, Graph, LabEx DRIIHM, Data qualification, Interdisciplinarity, Omics data, Decision Support Tools
fr
OHM Bassin Minier de Provence
|
DOI | 10.3897/tdwgproceedings.1.20740 |
Origine :
Fichiers éditeurs autorisés sur une archive ouverte
Loading...