63urn:lsid:arphahub.com:pub:0E0032F4-55AE-5263-8B3C-F4DD637C30C2Biodiversity Information Science and StandardsBISS2535-0897Pensoft Publishers10.3897/tdwgproceedings.1.20740207407928Conference AbstractSymposium: Using Big Data Techniques to Cross Dataset Boundaries - Integration and Analysis of Multiple DatasetsIndexMEED cases studies using "Omics" data with graph theoryDavidRomainromain.david@imbe.frhttps://orcid.org/0000-0003-4073-74561FéralJean-Pierre1ArchambeauAnne-Sophie2ArnaudFanny3AuberDavid4BaillyNicolashttps://orcid.org/0000-0003-4994-06535BernardLoup6Berti-EquilleLaure7BlanpainCyrille8BretonVincent9Chenuil-MaurelAnne10Cohen NabeiroAnna11DiasAlrick12DelavaudAurélie13GoffaudRobin14GachetSophie10GibertKarina15Herrera FernandezManuel16HogieLuc17IencoDino18JulliardRomain19Le BrasYvan20LecubinJulien21LegreYannick22LeydetMichelle23LoisGrégoire24MadonBénédicte25MarchalFrançois26Mendez MunozVictor27MeunierJean-Charles28MihoubJean-Baptiste20MougenotIsabelle29PamerlonSophie30PeletierEric31RomierGeneviève32Roux-MicholletDadhttps://orcid.org/0000-0002-4705-337533SpechtAlison34SuraceChristian35RaynalJean-Claude36TatoniThierry10Mediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon, Station Marine d’Endoume, Marseille, France, MetropolitanMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon, Station Marine d’EndoumeMarseilleFrance, MetropolitanGBIF France, Paris, France, MetropolitanGBIF FranceParisFrance, MetropolitanENS Lyon, OHM Vallée du Rhône, Lyon, France, MetropolitanENS Lyon, OHM Vallée du RhôneLyonFrance, MetropolitanLABRI, Bordeaux, France, MetropolitanLABRIBordeauxFrance, MetropolitanHellenic Centre for Marine Research (HCMR), Gouves, GreeceHellenic Centre for Marine Research (HCMR)GouvesGreeceARCHIMEDE-UMR 7044, Université de Strasbourg CNRS, Strasbourg, France, MetropolitanARCHIMEDE-UMR 7044, Université de Strasbourg CNRSStrasbourgFrance, Metropolitan IRD (ESPACE DEV U228) and LIF, Marseille, France, Metropolitan IRD (ESPACE DEV U228) and LIFMarseilleFrance, MetropolitanSIP OSU Pytheas, CNRS, Marseille, France, MetropolitanSIP OSU Pytheas, CNRSMarseilleFrance, MetropolitanIdGC – LPC, CNRS, France Grilles, Marseille, France, MetropolitanIdGC – LPC, CNRS, France GrillesMarseilleFrance, MetropolitanMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon,, Marseille, France, MetropolitanMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon,MarseilleFrance, MetropolitanECOSCOPE, FRB, Paris, France, MetropolitanECOSCOPE, FRBParisFrance, MetropolitanMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon,, Marselle, France, MetropolitanMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon,MarselleFrance, MetropolitanECOSCOPE, FRB, Marseille, FranceECOSCOPE, FRBMarseilleFranceECOSCOPE, FRB, Marseille, France, MetropolitanECOSCOPE, FRBMarseilleFrance, MetropolitanDepartment of Statistics and Operations Research, Universitat Politecnica de Catalunya, Barcelona, SpainDepartment of Statistics and Operations Research, Universitat Politecnica de CatalunyaBarcelonaSpainEDEn - Dept. of Architecture and Civil Eng., University of Bath, Bath, United KingdomEDEn - Dept. of Architecture and Civil Eng., University of BathBathUnited Kingdom I3S (the laboratory of Computer Science of the University of Nice-Sophia Antipolis) and Inria, Nice, France, Metropolitan I3S (the laboratory of Computer Science of the University of Nice-Sophia Antipolis) and InriaNiceFrance, MetropolitanUMR TETIS, Montpellier, France, MetropolitanUMR TETISMontpellierFrance, MetropolitanMuseum of Natural History (MNHN), Paris, FranceMuseum of Natural History (MNHN)ParisFranceCESCO - Centre d'Écologie et des Sciences de la Conservation Muséum national d'Histoire naturelle, Paris, FranceCESCO - Centre d'Écologie et des Sciences de la Conservation Muséum national d'Histoire naturelleParisFranceSIP OSU Pytheas, Marseille, France, MetropolitanSIP OSU PytheasMarseilleFrance, MetropolitanEuropean Grill Infrastructure, Amsterdam, NetherlandsEuropean Grill InfrastructureAmsterdamNetherlandsMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’Avignon, Marseille, France, MetropolitanMediterranean Institute of Biodiversity and marine and terrestrial Ecology (IMBE), Aix Marseille Université/CNRS/IRD/Université d’AvignonMarseilleFrance, MetropolitanCESCO - Centre d'Écologie et des Sciences de la Conservation Muséum national d'Histoire naturelle, Paris, France, MetropolitanCESCO - Centre d'Écologie et des Sciences de la Conservation Muséum national d'Histoire naturelleParisFrance, MetropolitanUniversité Bretagne Occidentale IUEM, Brest, France, MetropolitanUniversité Bretagne Occidentale IUEMBrestFrance, MetropolitanUMR 7268 ADES - Anthropologie Bioculturelle, Droit, Ethique et Santé Université d'Aix-Marseille / CNRS / EFS, Marseille, France, MetropolitanUMR 7268 ADES - Anthropologie Bioculturelle, Droit, Ethique et Santé Université d'Aix-Marseille / CNRS / EFSMarseilleFrance, MetropolitanDepartment of Computer Architecture and Operating Systems (CAOS) Universitat Autònoma de Barcelona (UAB), Barcelona, SpainDepartment of Computer Architecture and Operating Systems (CAOS) Universitat Autònoma de Barcelona (UAB)BarcelonaSpainLAM / CeSAM, Marseille, France, MetropolitanLAM / CeSAMMarseilleFrance, MetropolitanUMR Espace DEV, Montpellier, Montpelier, France, MetropolitanUMR Espace DEV, MontpellierMontpelierFrance, MetropolitanGBIF France, Paris, FranceGBIF FranceParisFranceInstitut de Génomique - Genoscope - CEA, Paris, France, MetropolitanInstitut de Génomique - Genoscope - CEAParisFrance, MetropolitanIdGC, CNRS, France Grilles, Lyon, France, MetropolitanIdGC, CNRS, France GrillesLyonFrance, MetropolitanGRAIE, OHM Vallée du Rhône, Lyon, France, MetropolitanGRAIE, OHM Vallée du RhôneLyonFrance, MetropolitanCESAB, FRB, Aix en Provence, France, MetropolitanCESAB, FRBAix en ProvenceFrance, MetropolitanLAM, CNRS, Aix-Marseille Université, Marseille, France, MetropolitanLAM, CNRS, Aix-Marseille UniversitéMarseilleFrance, MetropolitanECCOREV FR3098, CNRS, Aix-Marseille Université, Marseille, France, MetropolitanECCOREV FR3098, CNRS, Aix-Marseille UniversitéMarseilleFrance, Metropolitan
Corresponding author: Romain David (romain.david@imbe.fr).
Academic editor:
2017010920171e20740BD85F54E-66BA-5157-BAE5-C819E06D7CBB90139531082017Romain David, Jean-Pierre Féral, Anne-Sophie Archambeau, Fanny Arnaud, David Auber, Nicolas Bailly, Loup Bernard, Laure Berti-Equille, Cyrille Blanpain, Vincent Breton, Anne Chenuil-Maurel, Anna Cohen Nabeiro, Alrick Dias, Aurélie Delavaud, Robin Goffaud, Sophie Gachet, Karina Gibert, Manuel Herrera Fernandez, Luc Hogie, Dino Ienco, Romain Julliard, Yvan Le Bras, Julien Lecubin, Yannick Legre, Michelle Leydet, Grégoire Lois, Bénédicte Madon, François Marchal, Victor Mendez Munoz, Jean-Charles Meunier, Jean-Baptiste Mihoub, Isabelle Mougenot, Sophie Pamerlon, Eric Peletier, Geneviève Romier, Dad Roux-Michollet, Alison Specht, Christian Surace, Jean-Claude Raynal, Thierry TatoniThis is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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.
InterdisciplinarityData qualificationOmics dataGraphThesaurusDecision Support Tools1-6 October 2017TDWG 2017 Annual ConferenceTDWG 2017Ottawa, CanadaData Integration in a Big Data Universe: Associating Occurrences with Genes, Phenotypes, and EnvironmentsPresenting author
Romain David
Funding program
Labex DRIIHM (OHM Bassin Minier de Provence, OHM Vallée du Rhône, OHM Littoral méditerranéen), Fédération ECCOREV FR 3098, OSU Pythéas, and LabEx OT Med
Hosting institution
CESAB, ECOSCOPE, FRB, GBIF, IMBE, LAM,
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