seadatacloud kick-off meeting
TRANSCRIPT
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French National Center for Scientific Research
Activities and links with SeaDataCloud
SeaDataCloud Kick-off meeting
Riga on November 30th 2016
Team work: Benoit Sautour, Philippe Bertrand, Arnaud Caillo, FabriceMendes, Vincent Hanquiez, Gérald Grégori, Melilotus Thyssen, Maurice Libes,
Mark Hoebeke, Nathalie Simon, Fabienne Rigaut-Jalabert, Pascal Claquin, Franck Delalee and Soumaya Lahbib
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I. Presentation
The principal organization for fundamental scientific
research in France (MENESR)
Through its 1100 Research unities and services, it
carries out research in all fields: Biology, Chemistry,
Ecology, Engineering, Social Sciences, Information
Sciences, Mathematics, Nuclear, Physics and Earth
Sciences & Astronomy (INSU).
CNRS-INSU elaborates, develops and coordinates
research and projects in astronomy, earth and
planetary science, space sciences and ocean and
atmosphere sciences.
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Activities:
- Researches on evolutionary
biology and ecology of aquatic
organisms.
- Participation in monitoring and
observation of the pelagic and
benthic environment in several
marine stations
Activities:
- Researches on oceanography:
Physics, Chemistry, Microbio,
Biogeochemistry and Ecology
- Researches on astronomy :
Physics, Chemistry
- Monitoring Services (SO) in
oceanography and astronomy
Activities:
- Researches on oceanography:
Physics, Chemistry, Microbio,
Biogeochemistry and Ecology
- Monitoring Service (SO) of
marine environnent.
Activities:
- Researches on marine
biology and ecology
- Monitoring and observation
of the pelagic and benthic
environment (time-series)
CaenRoscoff
Bordeaux
Marseille
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MarseilleGenova
Tunis
• MIO team: World leaders in H/L frequency observationusing FLOW CYTOMETRY (single cell level recordingsensor)
• MIO hosts the regional FCM platform “PRECYM” (2005) whichis the only cytometry platform certified by the GIS IBISA
• High frequency automated flow cytometry is successfullyimplemented on O/V (Marseille Tunis, Genova, Plymouth andRoscoff), Scientific Cruises and fixed stations (buoys).
• CYTOBASE database is dedicated to Flow Cytometry
datasets acquired by either automated or conventional
flow cytometer instruments.
• Autotrophic and heterotrophic microorganisms related to
functional groups. Cytobase keeps abundances, fluorescences,
Size estimation per functional group , (and images)
• FCM Data accessibility / a user-friendly web interface andhelpful tool for understanding several measurements at time.
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In situ automatedcytometer
BD Influx FACS Calibur
ASCII Data Table& Pictures
Acquisition Analysis Consolidation Expert QC (visual)
Inte
gration
Acce
ssibility
FCM Data management Workflow
Bentchtopflow
cytometers
CytoSenseM. Dugenne, 2015
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In situ automatedcytometer
BD Influx FACS Calibur
ASCII Data Table& Pictures
Acquisition Analysis Consolidation Expert QC (visual)
Inte
gration
Acce
ssibility
FCM Data management Workflow
Bentchtopflow
cytometers
CytoSenseM. Dugenne, 2015
https://chrome.mio.univ-amu.fr/chrome-cytobase/
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In situ automatedcytometer
BD Influx FACS Calibur
ASCII Data Table& Pictures
Acquisition Analysis Consolidation Expert QC (visual)
Inte
gration
Acce
ssibility
FCM Data management Workflow
Bentchtopflow
cytometers
CytoSenseM. Dugenne, 2015
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Met
adat
aD
ata
Cytobase Input Processor (Mathilde Dugenne, 2015)
© Tools developed by M. Dugenne, 2015
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Pic
ture
sel
ecti
on
Stat
ion
s Ex
plo
rer
Data Table
Picture Table© Tools developed by M. Dugenne, 2015
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• The OASU team hosts SOMLIT Database forcoastal monitoring (LHR) from 10 target in-situstations.
• Instruments: CTD Seabird and Niskin bottle.
• Datasets: Physico-Chemical and Biological(Chlorophyll and benchtop Flow cytometry)
• Accessibility / web-based interfaces : Highresolution, Low resolution for time series andCTD profiles.
SOMLIT for CTD measurements
http://somlit-db.epoc.u-bordeaux1.fr/bdd.php?serie=ST
http://somlit.epoc.u-bordeaux1.fr/fr/bdd.php
http://somlit.mio.univ-amu.fr/#/accueil
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Below detection limit
Not measured
Good
Questionable
Bad
Not reported
Good (mean of replicate measurements)
Good (not SOMLIT protocol)
No QC
Not sampled
0
1
2
3
4
5
6
7
8
9
Integration to SOMLIT DB
Format control
Quality control
Data entry
Data analysis
Data Acquisition
Quality flags
SOMLIT Data management Workflow
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• PELAGOS database is a collaborative work ofthe RESOMAR (National network of MarineStations)
• Instruments: Niskin Bottle and CTD Seabird
• Datasets: Coastal planktonic biodiversity(mostly time-series), microscopic counts andbenchtop Flow cytometry (with raw files)
• Area: mostly SOMLIT stations
• Management of species names in coherencewith WoRMS
• Access /user-friendly web interface for datauploading and downloading
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RESOMAR-PELAGOS Data management Workflow
BDD
PELAGOS web-based applicationRESOMAR laboratoriesData producer (human)
Data entry and qualification(.xls file, PELAGOS format)
Data acquisition- Microscopic counts- FCM dataset
in PELAGOS
Automatic Feed-backDetection of errors
Format controls
Taxa names linked to WoRMS AlPhia ID
(Login, password)
PELAGOS
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Physico-chemicalPlankton
FCM
Distribution to Pan-European SDC Portal of marine data management infrastructure
PELAGOSSOMLIT CYTOBASE
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Build and update FCM newcommon vocabularies
Set up a common datamanagement protocol andmethods for FCM with aspecial focus on QC
Work with a large FCM Community.
Adopt SDN QC flag scale andstandard vocabulary
Use SDC Best practices to generate standardized metadataand data : NEMO, Mikado, etc..
II. Links with SeaDataCloud
PELAGOS SOMLITCYTOBASE
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CNRS involvement
WP9.5.2 of the next SeaDataNet (VLIZ, CNRS,NERC-BODC and ICES): Ingesting, validating, long-term storage and access of Flow Cytometer data
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Thank you for your attention
Any questions?
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