LifeWatch - EGI Competence Centre EGI Community Forum Bari 2015 - - PowerPoint PPT Presentation

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LifeWatch - EGI Competence Centre EGI Community Forum Bari 2015 - - PowerPoint PPT Presentation

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LifeWatch - EGI Competence Centre EGI Community Forum Bari 2015 Observatories: VREs and Data portals LifewatchGreece Portal : Semantic web with Data services, Parallelizing R with RvLab, Manipulating specimens with MicroCT By Emmanouela

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LifeWatch - EGI Competence Centre

EGI Community Forum – Bari 2015

Observatories: VREs and Data portals LifewatchGreece Portal:

Semantic web with Data services, Parallelizing R with RvLab, Manipulating specimens with MicroCT

By Emmanouela Panteri

Contributors:N.Minadakis,Y.Marketakis, C.Bekiari, M.Doerr, A.Gougousis, A.Oulas, K.Keklikoglou, I.Filiopoulou, N.Michalakis, C.Arvanitidis

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LifeWatch Greece e-infrastructure

LWG e-infrastructure:

  • Multi-server e-infrastructure currently

deployed in HCMR, Crete

  • Hosts biodiversity data and applications

Applications:

  • e-services: searching datasets/ data or
  • ne-shot analyses
  • vLabs: interfaces for advanced

selection of datasets/data, and more elaborated suites of analyses

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Accessed by: LifeWatch Greece Portal

https://portal.lifewatchgreece.eu/

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Accessed by: LifeWatch Greece Portal

https://portal.lifewatchgreece.eu/

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LifeWatch Greece Portal vLabs

Semantic web with Data services Parallelizing R with RvLab Manipulating specimens with MicroCT

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The Problem

Main characteristics of biodiversity data:

  • its cross-disciplinary character.
  • Extremely broad range of data types

and structures.(xls, csv, DwC Archives etc)

  • Broad variety of semantic concepts

which encompasses.

  • It remains widely distributed and

unconnected.

http://metacatalogue.portal.lifewatchgreece.eu/

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The goal

Our goal in the context of LWGreece:

  • Support cataloguing and

publishing of all the relevant meta- data information of the Greek biodiversity domain.

  • Integrate data from heterogeneous

sources by supporting the definitions

  • f appropriate models.
  • Efficiently discover biodiversity

data of interest and provide replies to complex queries that could not be answered from the individual sources.

http://metacatalogue.portal.lifewatchgreece.eu/

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The idea

http://metacatalogue.portal.lifewatchgreece.eu/

Exploit the events’ information that is explicitly or implicitly contained in the datasets, model the different concepts and entities of the biodiversity domain and take advantage of the semantic graph’s capabilities to navigate efficiently through the different contents and discover data of interest.

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Design and implementation

3 Components Architecture: 1) Directory Service 2) Metadata Repository 3) Content Storage More than 20 Web Services. 1) Publishing Metadata/Data 2) Searching Metadata 3) Discovering Data 4) Browsing Services 5) Mapping Services 6) Transforming Metadata 7) Annotation Services

http://metacatalogue.portal.lifewatchgreece.eu/

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Search Data

http://metacatalogue.portal.lifewatchgreece.eu/

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Publish data

http://metacatalogue.portal.lifewatchgreece.eu/

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LifeWatch Greece Portal vLabs

Semantic web with Data services Parallelizing R with RvLab Manipulating specimens with MicroCT

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R Virtual-LABoratory basics

  • Ecological/biological interest
  • Offer statistical and visualization tools for LifeWatch ESFRI, using R

statistical language. Main Objective:

  • Optimize certain VEGAN package functions (Community Ecology

Package), which supports, clustering and ordination methods, diversity analysis and other functions for community and vegetation ecologists. More specific issues addressed are:

  • Big data manipulation (overcome memory barriers)
  • Computational time speed-up (task segmentation multi-cores, cluster

computing environment at HCMR – recently upgraded from LlifeWatch)

  • Develop an efficient and friendly user interface for analysis of ecological

community data.

http://rvlab.portal.lifewatchgreece.eu/

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RvLAB file types

http://rvlab.portal.lifewatchgreece.eu/

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RvLAB main page

http://rvlab.portal.lifewatchgreece.eu/

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RvLAB main page

http://rvlab.portal.lifewatchgreece.eu/

Workspace area Submitted Jobs area Functions area

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RvLAB functions

http://rvlab.portal.lifewatchgreece.eu/

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RvLAB Jobs

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RvLAB Jobs results

Jobs Results

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LifeWatch Greece Portal vLabs

Semantic web with Data services Parallelizing R with RvLab Manipulating specimens with MicroCT

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Micro-Computed Tomography

Exterior parts Interior parts MicroCT offers:

  • Collection of virtual galleries of scanned

taxa, displayed and disseminated

  • Manipulation of the 3D models through a

series of online tools

  • Ability to download the datasets for local

manipulations

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MicroCT main page

MicroCT main page Specimen Details

http://microct.portal.lifewatchgreece.eu/

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MicroCT offers

Medadata Video Visualisation

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LifewatchGreece Mobile Applications

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Mobile Applications

Citizen Science

MicroCT

medOBIS

RvLab

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RvLab Mobile app workflow

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MicroCT vlab Mobile app workflow

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Thank you