http://lod.bco-dmo.org/id/dataset/768655
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2019-05-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Estimated nitrate d15N modeled using an ensemble of artificial neural networks (EANNs)
2019-05-28
publication
2019-05-28
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-06-17
publication
https://doi.org/10.1575/1912/bco-dmo.768655.1
Patrick Rafter
University of California-Irvine
principalInvestigator
Aaron Bagnell
University of California-Santa Barbara
principalInvestigator
Timothy DeVries
University of California-Santa Barbara
principalInvestigator
Dario Marconi
Princeton University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Rafter, P., Bagnell, A., DeVries, T., Marconi, D. (2019) Estimated nitrate d15N modeled using an ensemble of artificial neural networks (EANNs). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-05-28 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.768655.1 [access date]
Estimated nitrate d15N Dataset Description: Methods and Sampling: <p>For complete methodology, refer to Rafter et al. (2019). In summary:</p>
<p><strong>Data Compilation:&nbsp;</strong>Nitrate d15N observations were compiled from studies dating from 1975 to 2018. This global ocean nitrate d15N database was interpolated using an ensemble of artificial neural networks (EANNs). For the compiled observed global ocean nitrate d15N data, see the related dataset: <a href="https://www.bco-dmo.org/dataset/768627" target="_blank">https://www.bco-dmo.org/dataset/768627</a></p>
<p><strong>Building the neural network model:</strong> We utilize an ensemble of artificial neural networks (EANNs) to interpolate our global ocean nitrate d15N database, producing complete 3D maps of the data. By utilizing an artificial neural network (ANN), a machine learning approach that effectively identifies nonlinear relationships between a target variable (the isotopic dataset) and a set of input features (other available ocean datasets), we can fill holes in our data sampling coverage of nitrate d15N.</p>
<p><strong>Binning target variables (Step 1):</strong> We binned the nitrate d15N observations to the World Ocean Atlas 2009 (WOA09) grid with a 1-degree spatial resolution and 33 vertical depth layers (0-5500 m). When binning vertically, we use the depth layer whose value is closest to the observation's sampling depth (e.g. the first depth layer has a value of 0 m, the second of 10 m, and the third of 20 m, so all nitrate isotopic data sampled between 0-5 m fall in the 0 m bin; between 5-15 m they fall in the 10 m bin, etc.). An observation with a sampling depth that lies right at the midpoint between depth layers is binned to the shallower layer. If more than one raw data point falls in a grid cell we take the average of all those points as the value for that grid cell. Certain whole ship tracks of nitrate d15N data were withheld from binning to be used as an independent validation set.</p>
<p><strong>Obtaining input features (Step 2):</strong> Our input dataset contains a set of climatological values for physical and biogeochemical ocean parameters that form a non-linear relationship with the target data. We have six input features including objectively analyzed annual-mean fields for temperature, salinity, nitrate, oxygen, and phosphate taken from the WOA09 (<a href="https://www.nodc.noaa.gov/OC5/WOA09/woa09data.html" target="_blank">https://www.nodc.noaa.gov/OC5/WOA09/woa09data.html</a>) at 1-degree resolution. Additionally, daily chlorophyll data from Modis Aqua for the period Jan-1-2003 through Dec-31-2012 is averaged and binned to the WOA09 grid (as described in Step 1) to produce an annual climatological field of chlorophyll values, which we then log transform to reduce their dynamic range.</p>
<p>The choice of these specific input features was dictated by our desire to achieve the best possible R2 value on our internal validation sets (Step 4). Additional inputs besides those we included, such as latitude, longitude, silicate, euphotic depth, or sampling depth either did not improve the R2 value on the validation dataset or degraded it, indicating that they are not essential parameters for characterizing this system globally. By opting to use the set of input features that yielded the best results for the global oceans, we potentially overlooked combinations of inputs that perform better at regional scales. However, given the scarcity of d15N data in some regions, it is not possible to ascribe the impact of a specific combination of input features versus the impact of available d15N data, which may not be representative of the region's climatological state, to the relative model performance in these regions.</p>
<p><strong>Training the ANN (Step 3):</strong> The architecture of our ANN consists of a single hidden layer, containing 25 nodes, that connects the biological and physical input features (discussed in Step 2) to the target nitrate isotopic variable (as discussed in Step 1). The role of the hidden layer is to transform input features into new features contained in the nodes. These are given to the output layer to estimate the target variable, introducing nonlinearities via an activation function. The number of nodes in this hidden layer, as well as the number of input features, determines the number of adjustable weights (the free parameters) in the network. For complete information, refer to Rafter et al. (2019).</p>
<p><strong>Validating the ANN (Step 4):</strong>To ensure good generalization of the trained ANN, we randomly withhold 10% of the d15N data to be used as an internal validation set for each network. This is data that the network never sees, meaning it does not factor into the cost function, so it works as a test of the ANN's ability to generalize. This internal validation set acts as a gatekeeper to prevent poor models from being accepted into the ensemble of trained networks (see Step 5). A second, independent or 'external' validation set, composed of complete ship transects from the high and low latitude ocean were omitted from binning in Step 1 and used to establish the performance of the entire ensemble. Our rationale for using complete ship transects is the following. If we randomly chose 10% of observations to perform an external validation, this dataset will be from the same cruises as the wider data. In other words, despite being randomly selected, the validating observational dataset will be highly correlated geographically. Contrast this with validating the EANN results with observations from whole research cruises in unique geographic regions—areas where the model has not "learned" anything about nitrate. We therefore argue that these observations from whole ship tracks therefore provide a more difficult test of the model.</p>
<p><strong>Forming the Ensemble (Step 5):&nbsp;</strong>The ensemble is formed by repeating Steps 3 to 4 (using a different random 10% validation set) until we obtain 25 trained networks for the nitrate d15N dataset. A network is admitted into the ensemble if it yields an R² value greater than 0.81 on the validation dataset.&nbsp;For complete information, refer to Rafter et al. (2019).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658392 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658392
completed
Patrick Rafter
University of California-Irvine
858-405-0539
31503 Shrewsbury Dr.
Laguna Beach
CA
92651
USA
prafter@uci.edu
pointOfContact
Aaron Bagnell
University of California-Santa Barbara
abagnell@ucsb.edu
pointOfContact
Timothy DeVries
University of California-Santa Barbara
805-893-5308
6804 Ellison Hall
Santa Barbara
CA
93106
USA
tdevries@geog.ucsb.edu
pointOfContact
Dario Marconi
Princeton University
609-424-7992
A15 Guyot Hall
Princeton
NJ
08544
USA
dmarconi@princeton.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
latitude
longitude
depth
d15N
d15N_stdev
theme
None, User defined
latitude
longitude
depth
d15N_NO3
featureType
BCO-DMO Standard Parameters
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative research: Combining models and observations to constrain the marine iron cycle
https://osprey.bco-dmo.org/project/766423
Collaborative research: Combining models and observations to constrain the marine iron cycle
<p><em>NSF Award Abstract:</em><br />
Tiny marine organisms called phytoplankton play a critical role in Earth's climate, by absorbing carbon dioxide from the atmosphere. In order to grow, these phytoplankton require nutrients that are dissolved in seawater. One of the rarest and most important of these nutrients is iron. Even though it is a critical life-sustaining nutrient, oceanographers still do not know much about how iron gets into the ocean, or how it is removed from seawater. In the past few years, scientists have made many thousands of measurements of the amount of dissolved iron in seawater, in environments ranging from the deep sea, to the Arctic, to the tropical oceans. They found that the amount of iron in seawater varies dramatically from place to place. Can this data tell us about how iron gets into the ocean, and how it is ultimately removed? Yes. In this project, scientists working on making measurements of iron in seawater will come together with scientists who are working on computer models of iron inputs and removal in the ocean. The goal is to work together to create a program that allows our computer models to "learn" from the data, much like an Artificial Intelligence program. This program will develop a "best estimate" of where and how much iron is coming into the ocean, how long it stays in the ocean, and ultimately how it gets removed. This will lead to a better understanding of how climate change will impact the delivery of iron to the ocean, and how phytoplankton will respond to climate change. With better climate models, society can make more informed decisions about how to respond to climate change. The study will also benefit a future generation of scientists, by training graduate students in a unique collaboration between scientists making seawater measurements, and those using computer models to interpret those measurements. Finally, the project aims to increase the participation of minority and low-income students in STEM (Science, Technology, Engineering, and Mathematics) research, through targeted outreach programs.</p>
<p>Iron (Fe) is an important micronutrient for marine phytoplankton that limits primary productivity over much of the ocean; however, the major fluxes in the marine Fe cycle remain poorly quantified. Ocean models that attempt to synthesize our understanding of Fe biogeochemistry predict widely different Fe inputs to the ocean, and are often unable to capture first-order features of the Fe distribution. The proposed work aims to resolve these problems using data assimilation (inverse) methods to "teach" the widely used Biogeochemical Elemental Cycling (BEC) model how to better represent Fe sources, sinks, and cycling processes. This will be achieved by implementing BEC in the efficient Ocean Circulation Inverse Model and expanding it to simulate the cycling of additional tracers that constrain unique aspects of the Fe cycle, including aluminum, thorium, helium and Fe isotopes. In this framework, the inverse model can rapidly explore alternative representations of Fe-cycling processes, guided by new high-quality observations made possible in large part by the GEOTRACES program. The work will be the most concerted effort to date to synthesize these rich datasets into a realistic and mechanistic model of the marine Fe cycle. In addition, it will lead to a stronger consensus on the magnitude of fluxes in the marine Fe budget, and their relative importance in controlling Fe limitation of marine ecosystems, which are areas of active debate. It will guide future observational efforts, by identifying factors that are still poorly constrained, or regions of the ocean where new data will dramatically reduce remaining uncertainties and allow new robust predictions of Fe cycling under future climate change scenarios to be made, ultimately improving climate change predictions. A broader impact of this work on the scientific community will be the development of a fast, portable, and flexible global model of trace element cycling, designed to allow non-modelers to test hypotheses and visualize the effects of different processes on trace metal distributions. The research will also support the training of graduate students, and outreach to low-income and minority students in local school districts.</p>
Fe Cycle Models and Observations
largerWorkCitation
project
eng; USA
oceans
-180
180
-79.5
83.5
2019-05-28
0
BCO-DMO catalogue of parameters from Estimated nitrate d15N modeled using an ensemble of artificial neural networks (EANNs)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/768667.rdf
Name: latitude
Units: degrees North
Description: <p>Latitude in degrees north</p>
http://lod.bco-dmo.org/id/dataset-parameter/768668.rdf
Name: longitude
Units: degrees East
Description: <p>Longitude in degrees East</p>
http://lod.bco-dmo.org/id/dataset-parameter/768669.rdf
Name: depth
Units: meters (m)
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/768670.rdf
Name: d15N
Units: per mil
Description: <p>modeled nitrate d15N</p>
http://lod.bco-dmo.org/id/dataset-parameter/768671.rdf
Name: d15N_stdev
Units: per mil
Description: <p>standard deviation</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
32254889
https://darchive.mblwhoilibrary.org/bitstream/1912/24277/1/dataset-768655_global-model-nitrate-d15n__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.768655.1
download
onLine
dataset
<p>For complete methodology, refer to Rafter et al. (2019). In summary:</p>
<p><strong>Data Compilation:&nbsp;</strong>Nitrate d15N observations were compiled from studies dating from 1975 to 2018. This global ocean nitrate d15N database was interpolated using an ensemble of artificial neural networks (EANNs). For the compiled observed global ocean nitrate d15N data, see the related dataset: <a href="https://www.bco-dmo.org/dataset/768627" target="_blank">https://www.bco-dmo.org/dataset/768627</a></p>
<p><strong>Building the neural network model:</strong> We utilize an ensemble of artificial neural networks (EANNs) to interpolate our global ocean nitrate d15N database, producing complete 3D maps of the data. By utilizing an artificial neural network (ANN), a machine learning approach that effectively identifies nonlinear relationships between a target variable (the isotopic dataset) and a set of input features (other available ocean datasets), we can fill holes in our data sampling coverage of nitrate d15N.</p>
<p><strong>Binning target variables (Step 1):</strong> We binned the nitrate d15N observations to the World Ocean Atlas 2009 (WOA09) grid with a 1-degree spatial resolution and 33 vertical depth layers (0-5500 m). When binning vertically, we use the depth layer whose value is closest to the observation's sampling depth (e.g. the first depth layer has a value of 0 m, the second of 10 m, and the third of 20 m, so all nitrate isotopic data sampled between 0-5 m fall in the 0 m bin; between 5-15 m they fall in the 10 m bin, etc.). An observation with a sampling depth that lies right at the midpoint between depth layers is binned to the shallower layer. If more than one raw data point falls in a grid cell we take the average of all those points as the value for that grid cell. Certain whole ship tracks of nitrate d15N data were withheld from binning to be used as an independent validation set.</p>
<p><strong>Obtaining input features (Step 2):</strong> Our input dataset contains a set of climatological values for physical and biogeochemical ocean parameters that form a non-linear relationship with the target data. We have six input features including objectively analyzed annual-mean fields for temperature, salinity, nitrate, oxygen, and phosphate taken from the WOA09 (<a href="https://www.nodc.noaa.gov/OC5/WOA09/woa09data.html" target="_blank">https://www.nodc.noaa.gov/OC5/WOA09/woa09data.html</a>) at 1-degree resolution. Additionally, daily chlorophyll data from Modis Aqua for the period Jan-1-2003 through Dec-31-2012 is averaged and binned to the WOA09 grid (as described in Step 1) to produce an annual climatological field of chlorophyll values, which we then log transform to reduce their dynamic range.</p>
<p>The choice of these specific input features was dictated by our desire to achieve the best possible R2 value on our internal validation sets (Step 4). Additional inputs besides those we included, such as latitude, longitude, silicate, euphotic depth, or sampling depth either did not improve the R2 value on the validation dataset or degraded it, indicating that they are not essential parameters for characterizing this system globally. By opting to use the set of input features that yielded the best results for the global oceans, we potentially overlooked combinations of inputs that perform better at regional scales. However, given the scarcity of d15N data in some regions, it is not possible to ascribe the impact of a specific combination of input features versus the impact of available d15N data, which may not be representative of the region's climatological state, to the relative model performance in these regions.</p>
<p><strong>Training the ANN (Step 3):</strong> The architecture of our ANN consists of a single hidden layer, containing 25 nodes, that connects the biological and physical input features (discussed in Step 2) to the target nitrate isotopic variable (as discussed in Step 1). The role of the hidden layer is to transform input features into new features contained in the nodes. These are given to the output layer to estimate the target variable, introducing nonlinearities via an activation function. The number of nodes in this hidden layer, as well as the number of input features, determines the number of adjustable weights (the free parameters) in the network. For complete information, refer to Rafter et al. (2019).</p>
<p><strong>Validating the ANN (Step 4):</strong>To ensure good generalization of the trained ANN, we randomly withhold 10% of the d15N data to be used as an internal validation set for each network. This is data that the network never sees, meaning it does not factor into the cost function, so it works as a test of the ANN's ability to generalize. This internal validation set acts as a gatekeeper to prevent poor models from being accepted into the ensemble of trained networks (see Step 5). A second, independent or 'external' validation set, composed of complete ship transects from the high and low latitude ocean were omitted from binning in Step 1 and used to establish the performance of the entire ensemble. Our rationale for using complete ship transects is the following. If we randomly chose 10% of observations to perform an external validation, this dataset will be from the same cruises as the wider data. In other words, despite being randomly selected, the validating observational dataset will be highly correlated geographically. Contrast this with validating the EANN results with observations from whole research cruises in unique geographic regions—areas where the model has not "learned" anything about nitrate. We therefore argue that these observations from whole ship tracks therefore provide a more difficult test of the model.</p>
<p><strong>Forming the Ensemble (Step 5):&nbsp;</strong>The ensemble is formed by repeating Steps 3 to 4 (using a different random 10% validation set) until we obtain 25 trained networks for the nitrate d15N dataset. A network is admitted into the ensemble if it yields an R² value greater than 0.81 on the validation dataset.&nbsp;For complete information, refer to Rafter et al. (2019).</p>
Specified by the Principal Investigator(s)
<p>See supplemental MatLab files:<br />
<a href="http://datadocs.bco-dmo.org/docs/Fe_Cycle_Models_and_Observations/data_docs/d15NO3_ANN.m" target="_blank"><strong>d15NO3_ANN.m</strong></a>&nbsp;-This script creates an ensemble of Artificial Neural Networks (ANNs) to interpolate delta15N of nitrate observations globally using ocean&nbsp;datasets from the World Ocean Atlas 2009.<br />
<a href="http://datadocs.bco-dmo.org/docs/Fe_Cycle_Models_and_Observations/data_docs/PR19_d15NO3_ANN_anclim_inputs.mat" target="_blank"><strong>PR19_d15NO3_ANN_anclim_inputs</strong></a> - input data for d15NO3_ANN.m<br />
<a href="http://datadocs.bco-dmo.org/docs/Fe_Cycle_Models_and_Observations/data_docs/PR19_d15NO3_ANN_anclim_outputs.mat" target="_blank"><strong>PR19_d15NO3_ANN_anclim_outputs</strong></a> - output of d15NO3_ANN.m&nbsp;</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact