IndexMEED cases studies using &#39;Omics&#39; data with graph theory

David, Romain; Feral, Jean-Pierre; Archambeau, Anne-Sophie; Arnaud, Fanny; Auber, David; Bailly, Nicolas; Bernard, Loup; Berti-Equille, Laure; Blanpain, Cyrille; Breton, Vincent; Chenuil-Maurel, Anne; Cohen Nabeiro, Anna; Dias, Alrick; Delavaud, Aur&#233;lie; Goffaud, Robin; Gachet, Sophie; Gibert, Karina; Herrera Fernandez, Manuel; Hogie, Luc; Ienco, Dino; Julliard, Romain; Le Bras, Yvan; Lecubin, Julien; Legre, Yannick; Leydet, Michelle; Lois, Gr&#233;goire; Madon, B&#233;n&#233;dicte; Marchal, Fran&#231;ois; Mendez Munoz, Victor; Meunier, Jean-Charles; Mihoub, Jean-Baptiste; Mougenot, Isabelle; Pamerlon, Sophie; Peletier, Eric; Romier, Genevi&#232;ve; Roux-Michollet, Dad; Specht, Alison; Surace, Christian; Raynal, Jean-Claude; Tatoni, Thierry

doi:10.3897/tdwgproceedings.1.20740

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Article: IndexMEED cases studies using 'Omics' data with graph theory

Title

IndexMEED cases studies using 'Omics' data with graph theory

By

David, Romain Feral, Jean-Pierre Archambeau, Anne-Sophie Arnaud, Fanny Auber, David Bailly, Nicolas Bernard, Loup Berti-Equille, Laure Blanpain, Cyrille Breton, Vincent Chenuil-Maurel, Anne Cohen Nabeiro, Anna Dias, Alrick Delavaud, Aurélie Goffaud, Robin Gachet, Sophie Gibert, Karina Herrera Fernandez, Manuel Hogie, Luc Ienco, Dino Julliard, Romain Le Bras, Yvan Lecubin, Julien Legre, Yannick Leydet, Michelle Lois, Grégoire Madon, Bénédicte Marchal, François Mendez Munoz, Victor Meunier, Jean-Charles Mihoub, Jean-Baptiste Mougenot, Isabelle Pamerlon, Sophie Peletier, Eric Romier, Geneviève Roux-Michollet, Dad Specht, Alison Surace, Christian Raynal, Jean-Claude Tatoni, Thierry

Type

Article

Date of Publication

2017-9-1

Original Publication

Metabarcoding and metagenomics

Volume

Pages

1--4

Subjects

Data qualification , Decision Support Tools , Graph , interdisciplinarity , Omics data , Thesaurus

Contributed by

Pensoft Publishers

Language

English

Published by

Bulgaria Pensoft Publishers 2017-

Identifiers

DOI: https://doi.org/10.3897/tdwgproceedings.1.20740

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License Type URL: https://creativecommons.org/licenses/by/4.0/
Rights: https://biodiversitylibrary.org/permissions
Copyright Status: In copyright. Digitized with the permission of the rights holder.
Rights Holder: Copyright held by individual article author(s).

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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.<br> 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.<br> 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.