Observatories: VREs and Data portals LifewatchGreece Portal : Semantic web with Data services, Parallelizing R with RvLab, Manipulating specimens with MicroCT

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LifeWatch - EGICompetence CentreEGI Community Forum – Bari 2015

Observatories: VREs and Data portals LifewatchGreece Portal:

Semantic web with Data services, Parallelizing R with RvLab,

Manipulating specimens with MicroCTBy 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

one-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




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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 of appropriate models.

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




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The idea


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




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Search Data




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Publish data




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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




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RvLAB main page




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RvLAB main page


Workspace area

Submitted Jobs area

Functions area



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RvLAB functions




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RvLAB Jobs

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RvLAB Jobs results

Jobs Results

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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

http://www.youtube.com/watch?v=lk9QjA20Gww

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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

Presentations & Public Speaking

Observatories: VREs and Data portals LifewatchGreece Portal : Semantic web with Data services, Parallelizing R with RvLab, Manipulating specimens with MicroCT