Dataset: GT10 - Spctrl_Absp

Name: Spectral absorption coefficients of phytoplankton along US GEOTRACES North Atlantic Transect from the R/V Knorr KN199-04 cruise in the subtropical N. Atlantic in 2010 (U.S. GEOTRACES NAT project)
Published: 2013-01-23
License: https://creativecommons.org/licenses/by/4.0/
Keywords: oceans

Cite This Dataset

Project:

U.S. GEOTRACES North Atlantic Transect (U.S. GEOTRACES NAT)

Principal Investigator:

Aimee Neeley (National Aeronautics and Space Administration, NASA)

Co-Principal Investigator:

Joaquin Chaves (National Aeronautics and Space Administration, NASA-JPL)

BCO-DMO Data Manager:

Danie Kinkade (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version Date:

2013-01-23

Validated:

Yes

Current State:

Final no updates expected

Data URL:

https://www.bco-dmo.org/dataset/3867/data

Spectral absorption coefficients of phytoplankton along US GEOTRACES North Atlantic Transect from the R/V Knorr KN199-04 cruise in the subtropical N. Atlantic in 2010 (U.S. GEOTRACES NAT project)

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Description

Phytoplankton spectral absorption coefficient (ap) from surface samples collected on Whatman, 2.5cm glass fiber filters (GFF). Samples were collected during Geotraces 2010 (kn199-04).

The following metadata was extracted from the header information from each file. Where necessary the information was incorporated into BCO-DMO metadata fields or retained in file (* and X represent file-specific values):

/begin_header
/affiliations=NASA_SSAI
/investigators=Aimee_Neeley Joaquin_Chaves
/contact=aimee.neeley@nasa.gov
/experiment=Geotraces
/cruise=kn199-4
/station=10
/data_file_name=F06_St*_AP.csv
/documents=F06_log.csv
/calibration_files=SeaBASS_NDFilter.pdf
/data_type=scan
/data_status=final
/start_date=201010XX
/end_date=201010XX
/start_time=XX:XX:00[GMT]
/end_time=XX:XX:00[GMT]
/north_latitude=XX.XXX[DEG]
/south_latitude=XX.XXX[DEG]
/west_longitude=XX.XXX[DEG]
/east_longitude=XX.XXX[DEG]
/measurement_depth=0.0
/water_depth=NA
!
!COMMENTS
!Samples were collected in duplicate using a peristaltic pump at the surface. Samples were collected in conjunction with AOP package deployments
!Duplicate samples are being reported here (rep numbers are in the field name)
!Samples were filtered under vacuum (~5-7psi) onto combusted GF/F filters
!See SeaBass_NDFilter.pdf for explanation of fields
!See F06_log.csv for metadata
!
/missing=-999
/delimiter=comma

Acquisition Description

The following information was obtained from file headers and via correspondence with PIs:

Samples were collected in duplicate, using a peristaltic pump at the surface and were filtered under vacuum (~5-7psi) onto combusted GF/F filters. Samples from station 1 were collected with WHOI's GEOTRACES pump. Sample numbers for stations > 1 were collected with NASA's surface peristaltic pump. Samples were collected in conjunction with AOP package deployments.

See Processing Description for a link to additional information.

Processing Description

For sample processing information and methodology, see associated SeaBASS documentation file.

BCO-DMO Processing notes:

Edits made:
- Parameter header names were edited to conform to BCO-dMO convention
- Blank data fields were edited to 'nd'
- Edited time to remove colons and drop unused seconds
- Edited precision of lat/lon to four decimals.
- Edited precision of absorbance, and respecctive absorbance standard deviation
    and absorption coefficient data to 8 decimals.
- Added columns for 'diameter' and 'volume_filtered' (previously in metadata log file)
- Removed the comment information from file headers. Where
    necessary the information was incorporated into BCO-DMO
    metadata fields and retained entirely in Dataset Description.

Note: The variable "abs_blank_sd" corresponds to standard deviation data for station 7 only, when sample processing spanned two days (abs_blank_sd was calculated at the end of each day). This parameter is displayed as 'nd' for all other stations where all processing was completed in one day.

Definitions of parameter name components obtained from PI:

ap=total particulate absorption
ad= detrital absorption
aph= phytoplankton absorption
ap-ad=aph

Correspondence with the Co-PI on 2013.01.12, necessitated editing the header note indicating NASA's pump. Therefore, this comment retained in the header has been edited to the following text:

#samples from station 1 were collected with WHOI's GEOTRACES pump
#sample numbers for stations greater than 1 were collected with NASA's
# surface peristaltic pump

Additional GEOTRACES Processing: After the data were submitted to the International Data Management Office, BODC, the office noticed that important identifying information was missing in many datasets. With the agreement of BODC and the US GEOTRACES lead PIs, BCO-DMO added standard US GEOTRACES information, such as the US GEOTRACES event number, to each submitted dataset lacking this information. To accomplish this, BCO-DMO compiled a 'master' dataset composed of the following parameters: station_GEOTRC, cast_GEOTRC (bottle and pump data only), event_GEOTRC, sample_GEOTRC, sample_bottle_GEOTRC (bottle data only), bottle_GEOTRC (bottle data only), depth_GEOTRC_CTD (bottle data only), depth_GEOTRC_CTD_rounded (bottle data only), BTL_ISO_DateTime_UTC (bottle data only), and GeoFish_id (GeoFish data only). This added information will facilitate subsequent analysis and inter comparison of the datasets.

Bottle parameters in the master file were taken from the GT-C_Bottle_GT10, GT-C_Bottle_GT11, ODF_Bottle_GT10, and ODF_Bottle_GT11 datasets. Non-bottle parameters, including those from GeoFish tows, Aerosol sampling, and McLane Pumps, were taken from the Event_Log_GT10 and Event_Log_GT11 datasets. McLane pump cast numbers missing in event logs were taken from the Particulate Th-234 dataset submitted by Ken Buesseler.

A standardized BCO-DMO method (called “join”) was then used to merge the missing parameters to each US GEOTRACES dataset, most often by matching on sample_GEOTRC or on some unique combination of other parameters.

If the master parameters were included in the original data file and the values did not differ from the master file, the original data columns were retained and the name of the parameters were changed from the PI-submitted names to the standardized master names. If there were differences between the PI-supplied parameter values and those in the master file, both columns were retained. If the original data submission included all of the master parameters, no additional columns were added, but parameter names were modified to match the naming conventions of the master file.

See the dataset parameters documentation for a description of which parameters were supplied by the PI and which were added via the join method.

More Information about this dataset

Funding Sources

Funding Source	Award Number
National Aeronautics & Space Administration	NNX09AN94G

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
KN199-04	GT10 USGT-NAT-2010 KN199-4 GNAT U.S. GEOTRACES NAZT Leg 1 knorr199-4/5 Section Cruise (GA03) 316N20101015 GA03	2010-10-15	R/V Knorr	William J. Jenkins (Chief Scientist) Dr Edward A. Boyle (Co-Chief Scientist) Dr Gregory Cutter (Co-Chief Scientist)	data info

Instruments

Perkin Elmer Lambda 35 Spectrophotometer

(more info)

Short Name: Perkin Elmer Lambda 35

Community Standard Description

Generic Description

The Lambda 35 is a double beam UV/Vis spectrophotometer from Perkin Elmer, packing pre-aligned Tungsten and Deuterium Lamps. It has a wavelength range of 190-1100nm and a variable bandwidth range of 0.5 to 4nm.

PI supplied instrument name: Perkin Elmer Lambda 35 Spectrophotometer

Dataset-specific description

Pump surface

(more info)

Short Name: Pump surface

Community Standard Description

Generic Description

A source of uncontaminated near-surface seawater pumped onto the deck of the research vessel that can be sampled and analyzed. This pumped seawater supply is from an over-the-side pumping system, and is therefore different from the vessel underway seawater system.

PI supplied instrument name: Pump surface

Dataset-specific description

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
wavelength	Wavelength (between 300-800nm) at which spectrophotometric scans were performed, with a 1nm data interval and 2nm Slit Band Width (SBW).	nm	wavelength_general
abs_ap_1	Raw particulate absorbance measurement (no null correction).	dimensionless	absorbance
abs_ap_1_sd	Standard deviation of 3 filter rotations of particulate absorbance measurements.	dimensionless	absorbance_sd
abs_ad_1	Raw detrital absorbance measurement of first replicate (no null correction).	degrees Celsius	absorbance
abs_ad_1_sd	Standard deviation of 3 filter rotations of detrital absorbance measuremenst.	dimensionless	absorbance_sd
diameter_1	Diameter of sample biomass on filter.	mm	diameter
volume_filtered_1	Volume filtered; samples were filtered under vacuum (~5-7psi) onto combusted GF/F filters.	ml	vol_filt
ap_1	Total particulate absorption coeffient (null correction included).	1/m	absorption_coefficient
ad_1	Detrital absorption coefficienct (null correction included).	1/m	absorption_coefficient
aph_1	Phytoplankton absorption coefficient (A_ph = A_p - A_d).	1/m	absorption_coefficient
abs_blank_sd	Standard deviation of absorbance of all blank filters measured throughout the analysis period. Note: files that contain both replicates and more than one column of blank error indicates that replicates were analyzed on different days.	dimensionless	absorbance_sd
abs_ap_2	Raw particulate absorbance measurement (no null correction).	dimensionless	absorbance
abs_ap_2_sd	Standard deviation of 3 filter rotations of particulate absorbance measurements.	dimensionless	absorbance_sd
abs_ad_2	Raw detrital absorbance measurement of first replicate (no null correction).	dimensionless	absorbance
abs_ad_2_sd	Standard deviation of 3 filter rotations of detrital absorbance measuremenst.	dimensionless	absorbance_sd
diameter_2	Diameter of sample biomass on filter.	mm	diameter
volume_filtered_2	Volume filtered; samples were filtered under vacuum (~5-7psi) onto combusted GF/F filters.	ml	vol_filt
ap_2	Total particulate absorption coeffient (null correction included).	1/	absorption_coefficient
ad_2	Detrital absorption coeffient (null correction included).	1/m	absorption_coefficient
aph_2	Phytoplankton absorption coefficient (A_ph = A_p - A_d).	1/m	absorption_coefficient
abs_blank2_sd	Standard deviation of absorbance of all blank filters measured throughout the analysis period. Note: files that contain both replicates and more than one column of blank error indicates that replicates were analyzed on different days.	dimensionless	absorbance_sd
station	Unique station identifier.	dimensionless	station
lat	Latitude component of geographic position where samples were collected.	decimal degrees	lat
lon	Longitude component of geographic position where samples were collected.	decimal degrees	lon
time_gmt	Time of sampling, reported in GMT.	hhmm	time_gmt
date_gmt	Date, recorded in GMT time.	yyyymmdd	date_gmt
depth	Sample depth in meters.	meters	depth

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Dataset: GT10 - Spctrl_Absp