Christos Arvanitidis · LifeWatch EU National Strategic Reference Framework Christos Arvanitidis...

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

arvanitidis@hcmr.gr

Executive Development Task Force

Chrysoula Bekiari bekiari@ics.forth.gr Martin Doerr martin@ics.forth.gr Nikos Minadakis minadakn@ics.forth.gr Eva Chatzinikolaou evachatz@hcmr.gr Nicolas Bailly nbailly@hcmr.gr Carlo Allocca carlo@hcmr.gr Tilemachos Bourtzis tbourtzis@gmail.com Sarah Faulwetter sarifa@hcmr.gr Niki Keklikoglou keklikoglou@hcmr.gr Jacques Lagnel lagnel@hcmr.gr Dimitra Mavraki dmavraki@hcmr.gr Matina Nikolopoulou snikolo@hcmr.gr Anastasis Oulas oulas@hcmr.gr Evangelos Pafilis pafilis@hcmr.gr Emmanouela Panteri emmipan@hcmr.gr Nikolas Pattakos pattakosn@hcmr.gr Christina Pavloudi cpavloud@hcmr.gr Theodore Patkos patkos@ics.forth.gr Kostas Varsos varsosk@ics.forth.gr Vasilis Gerovasileiou vegerovas@hcmr.grGeorge Perantinos gper@hcmr.grNikitas Michalakis nikitas@hcmr.grIrene Filiopoulou filiop@hcmr.gr

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

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)

Biodiversity is...

LifeWatch: the concept of RIs

LifeWatch: challenges

LifeWatch: the “data era”

LifeWatch: distributed infrastructure

LifeWatch: organization

LifeWatchGreece Project info

• Nov 2012-Dec 2015 (extension)

• Almost 4 MEuros

• 49 Research Institutions and Academic Departments

• 400 participants

What makes LifeWatchGreece?

• Human Network

• Physical Installations

• Equipment (mostly hardware)

• Software

• Data

LifeWatchGreece Concept

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

LifewatchGreece Web Site

www.lifewatchgreece.eu

LifewatchGreece Web portal

portal.lifewatchgreece.eu

• Deploy “R” environment

• Running on clusters

• Multivariate analysis

• Biodiversity indices

(e.g. HD, WFD, MSFD)

R Statistical Processing

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

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)

• Future Semantic Approach to Medobis (and to GBIFGreece)

SemMedObis

• GBIF National node

• Serves Greek biodiversity terrestrial data and metadata

• IPT

GBIF Greece

• 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)

• Biovel workflow for invasive species modelling in the Mediterranean Basin

• Add Maritime Traffic Data

Ecological Niche Modeling

Ontology Management Environment

• MarineTLO Ontology Integrates data and metadata from different sources

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®

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.

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

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

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: info@lifewatchgreece.eu

Contribute and publish your own data and metadata

Thank you for your attention

http://www.lifewatchgreece.eu info@lifewatchgreece.eu