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European Union G. S. Research & Technology Hellenic Centrefor Marine Research
European Strategy Forumfor Research Infrastructures
LifeWatch EU National StrategicReference Framework
Christos ArvanitidisProject Coordinator
Foundation for Research and Technology - Hellas
11th Panhellenic Symposium of Oceanography & Fisheriesry 15-16 May, 2015
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Executive Development Task Force
Chrysoula Bekiari [email protected] Martin Doerr [email protected] Nikos Minadakis [email protected] Eva Chatzinikolaou [email protected] Nicolas Bailly [email protected] Carlo Allocca [email protected] Tilemachos Bourtzis [email protected] Sarah Faulwetter [email protected] Niki Keklikoglou [email protected] Jacques Lagnel [email protected] Dimitra Mavraki [email protected] Matina Nikolopoulou [email protected] Anastasis Oulas [email protected] Evangelos Pafilis [email protected] Emmanouela Panteri [email protected] Nikolas Pattakos [email protected] Christina Pavloudi [email protected] Theodore Patkos [email protected] Kostas Varsos [email protected] Vasilis Gerovasileiou [email protected] Perantinos [email protected] Michalakis [email protected] Filiopoulou [email protected]
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Data Managers
Antonios Avgoustinos - University of IoanninaEvangelia Avramidou - Aristotle University of Thessaloniki - Faculty of Agriculture, Forestry and Natural EnvironmentPanagiotis Damianidi - Aristotle University of Thessaloniki - School of BiologyPanagiotis Dimitriou-Nikolakis - University of Crete - Biology DepartmentAthanasios Evaggelopoulos - University of the Aegean - Department of Marine SciencesAlexandros Galanidis - University of the Aegean - Department of EnvironmentChristos Georgiadis - National and Kapodistrian University of Athens - Faculty of BiologyThemistoklis Giannoulis University of Thessaly - Department of Biochemistry & BiotechnologyAglaia Legaki National and Kapodistrian University of Athens - Faculty of BiologyDimitrios Likidis Democritus University of ThraceZoi Mylona Democritus University of Thrace - Department of Primary Level EducationEmmanouil Nikolakakis University of Crete - Natural History Museum CreteEleni Panagiotou University of Crete - Natural History Museum CreteGabriella Papastefanou National and Kapodistrian University of Athens - Faculty of BiologyPanagiota Paranou-Lioliou Aristotle University of Thessaloniki - School of BiologyManos Potiris Hellenic Centre for Marine Research - Institute of Marine Biology, Biotechnology and AquaculturePanagiota Stathopoulou University of Patras - Department of Environmental and Natural Resources ManagementIrini Tsikopoulou University of Crete - Biology DepartmentMarilena Tsompanou Hellenic Centre for Marine Research - Institute of Oceanography
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The field: biodiversity
…”the variability among living organisms from all sources including
inter-alia, terrestrial, marine and other aquatic ecosystems and the
ecological complexes of which they are part” (CBD)
….”includes diversity within species between species and
ecosystems”….. (Gaston & Spicer, 2004)
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Biodiversity is...
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LifeWatch: the concept of RIs
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LifeWatch: challenges
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LifeWatch: the “data era”
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LifeWatch: distributed infrastructure
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LifeWatch: organization
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LifeWatchGreece Project info
• Nov 2012-Dec 2015 (extension)
• Almost 4 MEuros
• 49 Research Institutions and Academic Departments
• 400 participants
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What makes LifeWatchGreece?
• Human Network
• Physical Installations
• Equipment (mostly hardware)
• Software
• Data
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LifeWatchGreece Concept
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LifeWatchGreece e-infrastructure
● Multi-servere-infrastructure currently deployed in HCMR, Crete
● Hosts biodiversity data and applications Applications:
● e-services: searching datasets/ data or one-shot analyses
● vLabs: interfaces for advanced selection of datasets/data, and more elaborated suites of analyses
Application development in 2 steps:● Independent development of a web
application (by the team or others)● Integration to the infrastructure / portal
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LifewatchGreece Web Site
www.lifewatchgreece.eu
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LifewatchGreece Web portal
portal.lifewatchgreece.eu
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• Deploy “R” environment
• Running on clusters
• Multivariate analysis
• Biodiversity indices
(e.g. HD, WFD, MSFD)
R Statistical Processing
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Micro-computed tomography Non-destructive method of 3D x-ray microscopy Creation of 3D models of objects from a series of x-ray projection images
MicroCT
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MedOBIS
• Marine species datasets and satellite data from Mediterranean.
• Geoserver store/publish maps and data
• Viewer based on OpenLayers
(Search by taxon, polygon, etc)
• Download results in various formats
(KLM,CSV,WMS,WFS) OGC Standards
• Medobis Integrated Publishing Toolkit (IPT)
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• Future Semantic Approach to Medobis (and to GBIFGreece)
SemMedObis
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• GBIF National node
• Serves Greek biodiversity terrestrial data and metadata
• IPT
GBIF Greece
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• Multiply Applications for Genomics and Bioinformatics
• Tools for analysis of next generation sequencing: Full genoms Metagenomics & microbial community Gene prediction Automatic annotation Phylogenetic analysis SNPs & SSRs mining
Genetics(+omics)
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• Biovel workflow for invasive species modelling in the Mediterranean Basin
• Add Maritime Traffic Data
Ecological Niche Modeling
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Ontology Management Environment
• MarineTLO Ontology Integrates data and metadata from different sources
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Data Management
• Data & Metadata Quality Control procedures (detect & manage taxonomic and spatial error, dates, measurements, missing information etc)
• Online taxon match tool(WORMS and PESI)
• Marine Regions, Getty Thesaurus of Geographic Names®
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Citizen Science & Mobile Applications
The number of the Citizen Science projects has been constantly rising the latest years, all over the world.
New tools for disseminating information and fast and easy internet access are the reasons why citizen scientists are now contributing more and more to projects on environmental monitoring or conservation biology and ecology. Citizen Science projects have recently been initiated, in collaboration with many partner institutions from all over Europe, and focus on the Mediterranean and Greek territories.
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What's up next?
Dynamical modelling vLab
Data publishing vLab (tube for manuscript submission in the BDJ (PENSOFT http://biodiversitydatajournal.com/)
Development of the Citizen Scientists Facility
Cell phone apps
Text mining vLab
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How much LifeWatchGreece is used?
EMBOS: use of Data Providers e-Services, MedOBIS and R vLabs
CIGESMED: use of the MedOBIS vLab, Citizen Scientists facility (possibly also the R Vlab)
EU BON: use of the MedOBIS and R vLabs, Citizen Scientists facility
MAPMED: use of the MedOBIS and R vLabs
WHP: use of the MedOBIS and R vLabs
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How can I participate?
Explore the web site: http://www.lifewatchgreece.eu
Inform us about your needs (methods of analysis, software, etc.)Your messages to: [email protected]
Contribute and publish your own data and metadata