EMODnet Chemistry WP2: Data aggregation and products generation - results, strengths and weaknesses - Atlantic Sea Annual Meeting, June 8-9 2016, Helsinki, Finland 1

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 8-9 2016, Helsinki, Finland 2

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 8-9 2016, Helsinki, Finland

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 8-9 2016, Helsinki, Finland

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 8-9 2016, Helsinki, Finland

Nitrate_plus_nitrite DIVA maps generation settings Atlantic area DIVA version 4.6.9 + weighting patch Time period 10-years running periods with yearly step for the 4 seasons Time range 1963-2014 Seasons Winter (0103), spring (0406), summer (0709), autumn (1012) Vertical layers IODE standards (30 levels) Nutrients at surface (0m) – summer (0709) - 20002009 Phosphate Nitrate_plus_nitrite Silicate Ammonium Annual Meeting, June 15-16 2015, Istanbul, Turkey

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 8-9 2016, Helsinki, Finland 7

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 8-9 2016, Helsinki, Finland 8

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 898LV12840015 44 errors in Local_cdi_id : hyphen missing 486PE15101A336881 instead of 486PE151-01A336881 92 wrong EDMO codes 2124 instead of 3288 Annual Meeting, June 8-9 2016, Helsinki, Finland 9

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 8-9 2016, Helsinki, Finland 10

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 8-9 2016, Helsinki, Finland

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 7782-44-7} 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 7782-44-7} 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 7782-44-7} 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 7782-44-7} per unit volume of the water body [dissolved plus reactive particulate phase] by in-situ Beckmann probe DOXYCZ01 Concentration of oxygen {O2 CAS 7782-44-7} 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 7782-44-7} 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

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 479-61-8} 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 479-61-8} 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 479-61-8} 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 479-61-8} 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 479-61-8} 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 479-61-8} 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 8-9 2016, Helsinki, Finland

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 8-9 2016, Helsinki, Finland

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 8-9 2016, Helsinki, Finland

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 8-9 2016, Helsinki, Finland

DIVA maps production DIVA maps settings : settings Atlantic area DIVA version 4.6.9 + weighting patch Time period 10-years running periods with yearly step for the 4 seasons Time range 1963-2014 Seasons spring (0406), summer (0709) Vertical layers IODE standards (30 levels) parameters Oxygen Annual Meeting, June 15-16 2015, Istanbul, Turkey

DIVA maps production Oxygen at surface (0m) – summer (0709) Annual Meeting, June 15-16 2015, Istanbul, Turkey

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 15-16 2015, Istanbul, Turkey

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 8-9 2016, Helsinki, Finland 20

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 8-9 2016, Helsinki, Finland 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 8-9 2016, Helsinki, Finland 22

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 8-9 2016, Helsinki, Finland 23

Thanks! Annual Meeting, June 8-9 2016, Helsinki, Finland

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 15-16 2015, Istanbul, Turkey 25