EURO-BASIN Cruise Data transfer to
PANGAEA
Janine Felden & Stéphane Pesant
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
1. EURO-BASIN cruise data
2. Data submission to PANGAEA
3. Editorial work at PANGAEA
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Workflow for Cruise Data to PANGAEA
What?
When?
Who?
How?
Meta-Data (Latitude;
DATA (experiments,
Longitude; Gear etc.)
measurements)
Immediately after
the expedition
needed to
georeference/
harmonize data
After final evaluation BUT
best before paper
submission !!!
Responsible
Scientist (PI)
Chief Scientist
PANGAEA Ticket System
OR
e-mail
me Felden
Cruise data transfer
– Janine
Annual EURO-BASIN meeting, 22. – 24.10.2013
Meta-Data in PANGAEA
Cruise / Responsible Scientist
2013
FS Maria Merian 'Trans-Atlantic‘ / Linda Holste
yes
RV Celtic Explorer 'Trans-Atlantic Acoustic Survey / Georg Rose
no
RV James Cook 'Porcupine Abyssal Plain 2013‘ / Richard Lampitt
no
G.O. Sars Trans-Atlantic / Geir Huse, W. Melle
©http://libraryjumpers.webs.com/
EURO-BASIN Cruises metadata
(2012/2013)
no/yes
CCGS Hudson (Labrador Monitoring Transect) / Eric Head
no
RV B. Saemundsson / A. Gislason
no
2012
FS METEOR 'Deep Convection' / Linda Holste
yes
RV Celtic Explorer, Trans-Atlantic Acoustic Survey / George Rose
no
RV B. Saemundsson / A. Gislason
no
G.O. Sars 'Svinoy Section‘ / Geier Huse
no
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Which Event-metadata are requested ?
•
•
•
•
•
Cruise (ship, start, end, chief scientist)
Latitude (start/end)
Longitude (start/end)
Date, Time (start/end)
Gear & additional metadata
– Nets (type, mesh size, minimum/maximum water depths, volume
filtered ...)
– CTD & water samples (filtered volume...)
Ship station list and cruise report usually
contains most of the relevant metadata
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Data submission via
Online ticket system (JIRA Client): http://www.pangaea.de/submit/
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Data submission via
Online ticket system (JIRA Client):
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Data submission via
Online ticket system (JIRA Client):
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Ticket system workflow
Author submit data
(open issue)
Data librarian
assigns curator
are informed
Curator
preparation of
data set
communication via
ticket system (mail)
Data are
Author
Data set is citable via DOI
(http://doi.pangaea.de/10.159
4/PANGAEA.xxx) & can be
linked to publisher (e.g.
Elsevier) webpage
uploaded
Data are
published
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Data Publication
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Editorial work of WP1: Harmonization of cruise data
•
harmonization of metadata and data (geographical positions,
gear details etc., labeling)
• data set structuring to enhance future comparability
CTD with water
sampler
CDT - data
nutrient
water
sample
plankton
abundance
All have the same
meta data and
linked via the same
Eventlabel
experiments
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Editorial work of WP1: Data set review
Metaheader of dataset (open access):
 Citation: Title & Authors
 Reference: Link to publication
 Abstract: Short description of sampling/experimental set up/method
related to the data set (often not identical to paper abstract!)
 Events: Metadata of sampling event
 Parameter table: Overview of parameter measured, method used, PIs,
other parameter specific details
Data matrix can be password protected on request!!!
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Editorial work of WP1: Data set review
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Data set in PANGAEA
Almeda, R; Alcaraz, M; Calbet, A et al. (2011): Metabolic rates and carbon budget of early developmental stages of the marine cyclopoid
copepod Oithona davisae. Limnology and Oceanography
Auel, H; Werner, I (2003): Feeding, respiration and life history of the hyperiid amphipod Themisto libellula in the Arctic marginal ice zone
of the Greenland Sea. Journal of Experimental Marine Biology and Ecology
Belail, R; Leaute, J-P; Mahe, J-C et al. (2013): Survey bottom trawl data of Micromesistius poutassou (blue whiting) in Bay of Biscay and
Celtic Sea from the EVHOE time series (1997-2011)
Bode, A (2013): Biomasses and stable isotopes (carbon, nitrogen) in various plankton size fractions from the upper 200 m of the water
column along a zonal transect at approximatly 24°N
Bode, A; Alvarez-Ossorio, MT; Miranda, A et al. (2013): Zooplankton abundance for two shelf stations off Galicia (NW Spain) from 1994
to 2006
Buskey, EJ; Coulter, CJ; Brown, SL (1994): Feeding, growth and bioluminescence of the heterotrophic dinoflagellate Protoperidinium
huberi. Marine Biology
Buskey, EJ; Hyatt, CJ (1995): Effects of the Texas (USA) 'brown tide' alga on planktonic grazer. Marine Ecology Progress Series
De La Rocha, CL (2013): Mesocosm Experiment in the Bay of Hopavagen, Norway, August 2012
Doray, M; Massé, J; Bellois, P et al. (2013): Micromesistius poutassou (blue whiting) abundance and biomass data in Bay of Biscay
estimated from acoustic surveys (2000-2012)
Hänselmann, K; Walter, B (2013): Microzooplankton grazing experiment during Maria S. Merian cruise MSM26
Harmer, RA; Lindeque, PK (2013): Effect of elevated temperature on egg production, grazing and mortatlity of Calanus finmarchicus in
the North Atlantic
Holste, L (2013): Zooplankton biomass data METEOR cruise M87/1
Huse, G (2013): Spatially explicit estimates of length and biomass of Clupea harengus (Norwegian spring spawning herring) from acoustic
and trawl surveys in the North-East Atlantic in May 2012
Jónasdóttir, SH; Nielsen, TG (2013): Egg production, hatching, faecal pellet production of Calanus finmarchicus in the North Atlantic
Möller, KO; Reichelt, T; Holste, L (2013): Physical oceanography during Maria S. Merian cruise MSM26
Möller, KO; Reichelt, T; Holste, L (2013): Physical oceanography during METEOR cruise M87/1 (Deep Convection Cruise)
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Data set in PANGAEA
Nielsen, KE (2013): In situ egg and fecal pellet volume measurements
Nielsen, KE (2013): In situ experiment Calanus finmarchicus egg production and grazing rates using fecal pellet production as proxy
Nielsen, KE (2013): In situ experiment on Calanus finmarchicus egg production and grazing rates using fecal pellet production as proxy.
North Atlantic spring 2013
Pinnegar, JKP; Trenkel, V; Melle, W et al. (2013): Stomach content records for pelagic fish (herring, mackerel, blue whiting, albacore and
bluefin tuna) in the northeast Atlantic
Sailley, S; Buitenhuis, ET (2013): Data compilation of dinoflagellate grazing and gross gowth efficiency rates from field and labratory
experiments
Swalethorp, R; Kjellerup, S; Nielsen, TG (2013): Mesozooplankton biomass data from the Kapisigdlit an inner fjord branch of the
Godthaabsfjord system, West Greenland, 2010
Swalethorp, R; Kjellerup, S; Nielsen, TG (2013): Mesozooplankton size data from the fjord branch Kapisigdlit located in the
Godthaabsfjord system, West Greenland, 2010
Swalethorp, R; Kjellerup, S; Nielsen, TG (2013): Mesozooplankton abundance data from the fjord branch Kapisigdlit located in the
Godthaabsfjord system, West Greenland, 2010
Swalethorp, R; Kjellerup, S; Nielsen, TG (2013): Mesozooplankton abundance data from Disko Bay, West Greenland, 2008
Swalethorp, R; Kjellerup, S; Nielsen, TG (2013): Mesozooplankton biomass data from Disko Bay, West Greenland, 2008
Swalethorp, R; Kjellerup, S; Nielsen, TG (2013): Mesozooplankton size data from Disko Bay, West Greenland, 2008
Torres-Valdes, S; Painter, S; Martin, A et al. (2013): Compilation of downward flux observations from sediment trap deployments in the
Atlantic Ocean - Contribution to EURO-BASIN's Data integration
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013
Sum up
• Cruise metadata should be immediately submitted to
PANGAEA
• All EURO-BASIN validated data should be submitted to
PANGAEA
! PANGAEA data quantity & quality depends on the
data that are provided by the scientist !
http://www.pangaea.de/submit/
Thus:
• support the work of EUROBASIN WP1!
• for any data work including worries and ideas contact us
(Stéphane Pesant ([email protected]) or me ([email protected]))
Cruise data transfer – Janine Felden
Annual EURO-BASIN meeting, 22. – 24.10.2013