1. EMODnet Chemistry WP2: Data aggregation and products generation
- results, strengths and weaknesses -
Atlantic Sea
Annual Meeting, June , Helsinki, Finland 1

2. Outline Summary of results on Nutrients : Data inventory
Regional data buffer : time/space distribution
DIVA maps generation
Results on Other parameters (Oxygen and Chlorophylla)
Data inventory / aggregation / QC
Regional data buffer : space/time distribution by parameter
Contaminants : Data inventory
Strengths and weaknesses
Annual Meeting, June , Helsinki, Finland 2

3. Nitrate_plus_nitrite
Nutrients inventory
First harvesting
Second harvesting
Enlarged
data coverage
Distribution by partners
Nb CDIs
IEO
Ifremer
IHPT
RIHMI-NODC
IMR
UniHB
Total
15402
6505
4553
4492 36 9
Distribution by parameters
Nb CDIs
Phosphate
Nitrate_plus_nitrite
Silicate
Ammonium
Total
11319
7472
7110
5001
Annual Meeting, June , Helsinki, Finland

4. Nitrate_plus_nitrite
Regional data buffer
- Nutrients -
Time distribution
Nb CDIs
Phosphate
Nitrate_plus_nitrite
Silicate
Ammonium
Total
11319
7472
7110
5001
Time histograms
1970
1990
1990
1990
Season histograms
Annual Meeting, June , Helsinki, Finland

5. Nitrate_plus_nitrite
Regional data buffer
- Nutrients -
Space distribution
Nb CDIs
Phosphate
Nitrate_plus_nitrite
Silicate
Ammonium
Total
11319
7472
7110
5001
Station maps
Vertical plots
3000m
Annual Meeting, June , Helsinki, Finland

6. Nitrate_plus_nitrite
DIVA maps generation
settings
Atlantic area
DIVA version
weighting patch
Time period
10-years running periods with yearly step for the 4 seasons
Time range
Seasons
Winter (0103), spring (0406), summer (0709), autumn (1012)
Vertical layers
IODE standards (30 levels)
Nutrients at surface (0m) – summer (0709)
Phosphate
Nitrate_plus_nitrite
Silicate
Ammonium
Annual Meeting, June , Istanbul, Turkey

7. Other parameters inventory
Distribution by EDMO code
EDMO Code
Name
Country
Nb of CDIs 43
BODC
England
2575 96
GOD
Germany 1
134
CNR
Italy 3
353
IEO
Spain
6660
486
IFREMER
France
8926
590
IHPT
Portugal
629
612
IMR
Norway 12
681
RIHMI
Russian Federation
8812
691
INRH
Morocco 54
730
ICES
Denmark 37
3234
PANGAEA
364
3288
IPMA
911
Total
28584
Annual Meeting, June , Helsinki, Finland 7

8. Other parameters inventory
Distribution by parameters
Nb CDIs
Oxygen
Chlorophyll-a PH
Tot. Alkal.
DOC
BODC 43
1351
6871
GOD 96 1
CNR 134 3
IEO 353
5164
2211
599
164
IFREMER 486
5258
3860
102 18
IHPT 590
315
314
IMR 612 12
RIHMI 681
8800
4026
141
INRH 691 52 51
ICES 730 37 6
PANGAEA 3234
118 38
IPMA 3288
Total
21098
13357
5048
323
Annual Meeting, June , Helsinki, Finland 8

9. Other parameters - metadata QC -
ODV files harvested : problems faced (1)
116 empty files
semantic and column headers but no data
4026 errors on P01 for PH : white space character instead of XX
//<subject>SDN:LOCAL:pH</subject><object>SDN:P011::PH ZZXX</object>
3 errors in column header : white space missing
Depth [m] QV:SEADATANET DOXY_DOXSEB_NOT_NDT[ml/l]
33 errors in cruise name
Cruise Station
UPWELLING V CAP 7402 "NAN 00010
9 wrong Local_cdi_id
LIVRA_00400_G02 instead of 898LV
44 errors in Local_cdi_id : hyphen missing
486PE15101A instead of 486PE151-01A336881
92 wrong EDMO codes
2124 instead of 3288
Annual Meeting, June , Helsinki, Finland 9

10. Other parameters - metadata QC -
ODV files harvested : problems faced (2)
>1500 Incorrect primary variables (P01) :
- For sediment data, ADEPZZ01 instead of COREDIST
- For ocean data, RECORD number instead of ADEPZZ01
//SDN_parameter_mapping
//<subject>SDN:LOCAL:Record_No</subject><object>SDN:P01::ACYCAA01>
Many Warnings on SDN vocabulary version
//<subject>SDN:LOCAL:pH</subject><object>SDN:P011::PH ZZXX</object>
Solution : feedback loop with CDI partners
Files corrected locally by RL to gain time
Contact with the CDI partner to update the CDI in SDN/Emodnet infrastructure (MARIS CDI support)
Annual Meeting, June , Helsinki, Finland 10

11. Data aggregation and QC
- Other parameters -
Perform QC with ODV
Use only data with Quality Flag = 0, 1, 2, 6 as initial collection to use only good data
Unit conversion and aggregation (P35 vocabs)
Search for out of range values with Flag = 1
Set a QC for all measurements with Flag = 0
Set default values with Flag = 0, 1 to Flag = 9
Flag 0
Wrong Flag 9
Write a report on QC and send results to data providers and MARIS
Wrong Flag 1
Annual Meeting, June , Helsinki, Finland

12. Data aggregation Mix of uncalibrated and calibrated measurements
Oxygen data
SDN:P35::EPC00002: Water body dissolved oxygen concentration [umol/l]
Local parameter
P01 code
P06 code
P01 label
DOX1 [ml/l]
DOXYZZXX
UMLL
Concentration of oxygen {O2 CAS } per unit volume of the water body [dissolved plus reactive particulate phase]
Dissolved Oxygen [ml/l]
DOXY [umol/l]
UPOX
Oxygene [ml/l]
Oxygen [umol/l]
WC_dissO2_uncalib [umol/l]
DOXYSU01
Concentration of oxygen {O2 CAS } per unit volume of the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and no calibration against sample data
DOXY_DOXSEB_NOT_NDT [ml/l]
DOXYSC01
Concentration of oxygen {O2 CAS } per unit volume of the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and calibration against sample data
WC_dissO2_calib [umol/l]
Oxygen [ml/l]
WC_dissO2 [umol/l]
DOXYPR01
Concentration of oxygen {O2 CAS } per unit volume of the water body [dissolved plus reactive particulate phase] by in-situ Beckmann probe
DOXYCZ01
Concentration of oxygen {O2 CAS } per unit volume of the water body [dissolved plus reactive particulate phase] by in-situ sensor and calibration against sample data
DOX2 [umol/kg]
DOXMZZXX
KGUM
Concentration of oxygen {O2 CAS } per unit mass of the water body [dissolved plus reactive particulate phase]
Oxygen [umol/kg]
DissO2_Mass [umol/kg]
DOXY [umol/kg]
Mix of uncalibrated and calibrated measurements

13. Data aggregation Mix of uncalibrated and calibrated measurements
Chlorophyll-a data
SDN:P35::EPC00105: Water body chlorophyll-a [mg/m^3]
Local parameter
P01 code
P01 label
CPHL [mg/m^3]
CPHLZZXX
Concentration of chlorophyll-a {chl-a CAS } per unit volume of the water body [particulate >unknown phase]
Chlorophyll [mg/m^3]
CPWC [mg/m^3]
chl-a_water_NTTFfluor_manufctrcal [mg/m^3]
CPHLUMTF
Concentration of chlorophyll-a {chl-a CAS } per unit volume of the water body [particulate >unknown phase] by through-flow fluorometer plumbed into non-toxic supply and manufacturer's calibration applied
chl-a_water_ISfluor_sampcal [mg/m^3]
CPHLPS01
Concentration of chlorophyll-a {chl-a CAS } per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and calibration against sample data
Chlorophyll a [mg/m^3]
CPHLPR01
Concentration of chlorophyll-a {chl-a CAS } per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer
chl-a_water_ISfluor [mg/m^3]
FLU2 [mg/m^3]
CPHLPM01
Concentration of chlorophyll-a {chl-a CAS } per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and manufacturer's calibration applied
chl-a_water_ISfluor_manufctrcal_sensor1 [mg/m^3]
chl-a_water_ISfluor_labcal [mg/m^3]
CPHLPL01
Concentration of chlorophyll-a {chl-a CAS } per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and laboratory calibration applied
Mix of uncalibrated and calibrated measurements
Annual Meeting, June , Helsinki, Finland

14. Oxygen quality checks – problems faced
Data aggregation and QC
Oxygen quality checks – problems faced
Low Oxygen profiles
e.g. flagged some BODC data to 4
Strange Oxygen data
e.g. delete PANGAEA profiles because of not calibrated Oxygen
Low historic data
French SHOM data flagged to 3
Oxygen profiles decrease to zero
Russian data flagged to 3/4
Annual Meeting, June , Helsinki, Finland

15. Regional data buffer Oxygen data Better time coverage 1963
a) Station map
b) Vertical plot
c) Time histogram
d) Data bins
e) X/Y distribution
f) Season histogram
Annual Meeting, June , Helsinki, Finland

16. Chloroplyll-a quality checks – problems faced
Data aggregation and QC
Chloroplyll-a quality checks – problems faced
High Chla data at depth
Feedback to the CDI partner : calibrated data? correction to apply? Flag to 3/4 ?
Annual Meeting, June , Helsinki, Finland

17. DIVA maps production DIVA maps settings : settings Atlantic area
DIVA version
weighting patch
Time period
10-years running periods with yearly step for the 4 seasons
Time range
Seasons
spring (0406), summer (0709)
Vertical layers
IODE standards (30 levels)
parameters
Oxygen
Annual Meeting, June , Istanbul, Turkey

18. DIVA maps production Oxygen at surface (0m) – summer (0709)
Annual Meeting, June , Istanbul, Turkey

19. DIVA maps production Oxygen at surface (0m) – summer (0709)
M36/5 cruise – sept 1996
Feedback to the CDI partner : calibrated data? shift to apply? Flag to 3 ?
Run DIVA after corrrection/flag of these 57 profiles
Annual Meeting, June , Istanbul, Turkey

20. Contaminants inventory
EDMO Code
Name
Country
Nb of CDIs 96
GOD
Germany 1
353
IEO
Spain
201
486
IFREMER
France
250
590
IHPT
Portugal
1064
730
ICES
Denmark 78
1022
BRGM
351
3234
PANGAEA
119
3288
IPMA
416
Total
2480
Annual Meeting, June , Helsinki, Finland 20

21. Contaminants - metadata QC - ODV files harvested : problems faced
319 wrong file extension : .txt instead of .zip
163 wrong semantic header
Wrong primary variable : ADEPZZ01 instead of COREDIST
Warnings on SDN vocabulary version
Update of P01/P02/P35 vocabularies before data aggregation
Annual Meeting, June , Helsinki, Finland 21

22. Contaminants - metadata QC - ODV files harvested : problems faced
319 wrong file extension : .txt instead of .zip
163 wrong semantic header
Wrong primary variable : ADEPZZ01 instead of COREDIST
Warnings on SDN vocabulary version
Update of P01/P02/P35 vocabularies before data aggregation
Annual Meeting, June , Helsinki, Finland 22

23. Ongoing work Finish QC on Chlorophyll, PH, …
Re-run DIVA for Oxygen after additional QC
DIVA for Chlorophyll
Contaminants collections
Import aggregated Qced collections and DIVA maps in Oceanbrowser and Sextant catalogue
Send report on metadata and data QC to CDI partners and to MARIS
Annual Meeting, June , Helsinki, Finland 23

24. Thanks!
Annual Meeting, June , Helsinki, Finland

25. DIVA validation loop DIVA maps production
Data extraction (and weighting)
Parameters optimization
Run analysis
Additional QC
Phosphate
Silicate
NO3+NO2
Ammonium
Oxygen
Chlorophyll
4D Netcdf files ready
If needed
Annual Meeting, June , Istanbul, Turkey 25