NASA/TM-2002-211617

The SeaWiFS Bio-Optical Archive and Storage System

(SeaBASS): Current Architecture and Implementation

Editors

Giulietta S. Fargion and Charles R. McClain

Authors

P. Jeremy Werdell and Sean W. Bailey

National Aeronautics and

Space Administration

Goddard Space Flight Center

Greenbelt, Maryland 20771
NASA/TM-2002-211617

The SeaWiFS Bio-Optical Archive and Storage System

(SeaBASS): Current Architecture and Implementation

Editors

Giulietta S. Fargion, Science Applications International Corporation, Beltsville, Maryland

Charles R. McClain, Goddard Space Flight Center, Greenbelt, Maryland

Authors

P. Jeremy Werdell, Science System and Applications Inc., Lanham, Maryland

Sean W. Bailey, Futuretech Corporation, Greenbelt, Maryland

National Aeronautics and

Space Administration

Goddard Space Flight Center

Greenbelt, Maryland 20771

September 2002

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iii

PREFACE

The purpose of this technical report is to provide current documentation of the Sensor

Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS)

Project activities, NASA Research Announcement (NRA) research status, satellite data

processing, data product validation, and field calibration. This documentation is necessary to

ensure that critical information is related to the scientific community and NASA

management. This critical information includes the technical difficulties and challenges of

validating and combining ocean color data from an array of independent satellite systems to

form consistent and accurate global bio-optical time series products. This technical report is

not meant as a substitute for scientific literature. Instead, it will provide a ready and

responsive vehicle for the multitude of technical reports issued by an operational project.

Satellite ocean color missions require and abundance of high quality in situ measurements

for bio-optical and atmospheric algorithm development and post-launch product validation

and sensor calibration. To facilitate the assembly of a global data set, the Sea-viewing Wide

Field-of-view (SeaWiFS) Project developed the SeaWiFS Bio-optical Archive and Storage

System (SeaBASS), a local repository for in situ data regularly used in their scientific

analyses. The system has since been expanded to contain data sets collected by the

SIMBIOS Project, as part of NRA-96-MTPE-04 and NRA-99-OES-99. SeaBASS is a well

moderated and documented archive for bio-optical data with a simple, secure mechanism for

locating and extracting data based on user inputs. Its holdings are available to the general

public with the exception of the most recently collected data sets. Extensive quality

assurance protocols, comprehensive data and system documentation, and the continuation of

an archive and relational database management system (RDBMS) suitable for bio-optical

data all contribute to the continued success of SeaBASS. This document provides and

overview of the current operational SeaBASS system.

Giulietta S. Fargion

Charles R. McClain
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TABLE OF CONTENTS

Chapter 1: Introduction 1

Chapter 2: SeaBASS Data and Access Policies 7

Chapter 3: The SeaBASS Data File Format 10

Chapter 4: Data Submission and Quality Control 21

Chapter 5: SeaBASS Architecture and RDBMS Design 30

Chapter 6: Data Access and Online Resources 35

Glossary 41

References 42
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Chapter 1

Introduction

1.1 Motivation and Philosophy

Experiences with past and present satellite

ocean color missions, such as the Coastal Zone

Color Scanner (CZCS) and Sea-viewing Wide

Field-of-view Sensor (SeaWiFS), demonstrate

the need for high quality in situ measurements

for bio-optical algorithm development and

satellite data product validation (Gordon et al.

1983, Evans and Gordon 1994, McClain et al.

1998, Hooker and McClain 2000). The

National Aeronautics and Space Administration

(NASA) SeaWiFS Project, for example, is

tasked with producing normalized water-leaving

radiances with an absolute accuracy of 5%

(Hooker and Esaias 1993), which requires

comparative, globally distributed in situ

radiometric measurements with accuracy finer

than 5%. The advent of additional missions,

such as the Moderate Resolution Imaging

Spectroradiometer (MODIS) and the Medium

Resolution Imaging Spectrometer (MERIS), and

the approach of future missions, including the

Global Imager (GLI) and the second

Polarization and Directionality of the Earth's

Reflectances (POLDER-2) instrument, further

underline the need for accurate, temporally and

geographically diverse samples of

oceanographic and atmospheric data.

Historically, the amount of data suitable for

algorithm development and satellite validation

activities has been limited due to a paucity of

simultaneous observations and the difficulty

associated with obtaining globally distributed

sampling (O^Reilly et al. 1998, Bailey et al.

2000). With regards to the latter, spatial biases

are often undesirable for satellite missions with

continuous global coverage. Due to their

required accuracy, these data are additionally

limited by biases introduced by varying

measurement and data processing techniques

(Hooker and Maritorena 2000, Hooker et al.

2001). As such, global, high quality, in situ data

sets are invaluable and prerequisite to advance

the field of ocean color.

To facilitate the assembly of a global biooptical data set, the SeaWiFS Project developed

the SeaWiFS Bio-optical Archive and Storage

System (SeaBASS), a local repository for in situ

radiometric and phytoplankton pigment data

used regularly in their scientific analyses

(Hooker et al. 1994). The system has since been

expanded to contain oceanographic and

atmospheric data sets collected by the NASA

Sensor Intercomparison and Merger for

Interdisciplinary Biological and Oceanic Studies

(SIMBIOS) Project (McClain et al. 2002), as

part of NASA Research Announcements (NRA)

NRA-96-MTPE-04 and NRA-99-OES-99,

which has aided considerably in minimizing

spatial bias and maximizing data acquisition

rates (McClain and Fargion 1999a and 1999b,

Fargion and McClain 2001 and 2002). The

SeaWiFS and SIMBIOS Project Offices (SPO)

currently share responsibility for the

maintenance of SeaBASS, including all design

modification and construction.

To develop consistency across multiple data

contributors and institutions, the SPO has

defined and documented a series of in situ data

requirements and sampling strategies that ensure

that any particular set of measurements will be

acceptable for bio-optical and atmospheric

correction algorithm development and ocean

color sensor validation (Mueller and Austin

1995, Fargion et al. 2001, Mueller et al. 2002a

and 2002b). In addition, the SPO has sponsored

a series of round-robin activities to establish and

advance the state of instrument calibration,

protocols, and traceability to radiometric

standards (Mueller 1993, Meister et al. 2002).

Data prepared using these techniques are

suitable for both verifying the radiometric

precision and stability of satellite-borne ocean

color sensors and validating the algorithms used

to relate the radiances to other geophysical

parameters.
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SeaBASS was designed to be a wellmoderated, maintained, and documented archive

of bio-optical data, easily accessed by all

authorized users, yet secure enough to restrict

access when necessary, with a simple

mechanism for locating and extracting data

based on user inputs. Its success relies upon the

application of sufficient quality assurance

protocols, comprehensive data and system

documentation, and the continuation of an

archive and relational database management

system (RDBMS) suitable for bio-optical data.

This document provides an overview of the

current operational SeaBASS system. The

design, protocols, and utilities described in this

report supercede all other versions described in

previous SeaBASS-related documents (Hooker

and Firestone 1994, Firestone et al. 1994,

Firestone and Hooker 2001, Werdell et al.

2000a, 2000b, 2002a, and 2002b).

1.2 Synopsis

As of this writing, SeaBASS includes data

collected by researcher groups at 43 institutions

(Figure 1.1), encompassing over 1,000

individual field campaigns and 30,000 biooptical data files (Figure 1.2). These data

include over 220,000 phytoplankton pigment

concentrations, 10,000 continuous depth

profiles, and 14,000 spectrophotometric scans

(Figure 1.3). Atmospheric data sets are

collected using instruments maintained in the

SIMBIOS instrument pool*

, several FastRotating Shadow-band Radiometers (FRSR)

deployed by the Brookhaven National

Laboratory under SIMBIOS (Reynolds et al.

2001), and 14 CIMEL sun photometers

contributed by the SIMBIOS Project to the

NASA Aerosol Robotic Network (AERONET)

(Holben et al. 2001) (Figure 1.1). These data

include over 13,000 discrete measurements of

aerosol optical thickness (AOT) and 111 FRSR

campaigns (Figure 1.4). The volume of biooptical data (hereafter used to describe both the

 

*

 As of August 2002, the SIMBIOS instrument pool

consists of 16 MicroTops sun photometers, 2 SIMBAD

radiometers, 2 SIMBADA radiometers, 2 PREDE Mark II

sun photometers, and 1 micropulse LIDAR.

oceanic and atmospheric data archived in

SeaBASS) is rapidly increasing, however, as

SIMBIOS US Science Team members are

contractually obligated to provide data to

SeaBASS (McClain and Fargion 1999a and

1999b, Fargion and McClain 2001 and 2002).

The volume is expected to increase further as

new and upcoming ocean color programs, for

example, those for MODIS and MERIS, begin

to require and collect validation data.

The full bio-optical data set includes

measurements of apparent and inherent optical

properties, phytoplankton pigment

concentrations, and other related oceanographic

and atmospheric data, such as water

temperature, salinity, stimulated fluorescence,

and AOT (refer to Chapter 3 for additional

details on standard data parameters archived in

SeaBASS). Data are collected using a number

of instrument packages, such as profilers and

handheld instruments, and manufacturers on a

variety of platforms, including ships and

moorings (Fargion and McClain 2002). Field

data are collected and prepared, whenever

possible, according to the protocols defined by

the SPO, as referred to in section 1.1 and

Chapter 4 of this document (see also Mueller

and Austin 1995, Fargion et al. 2001, Mueller et

al. 2002a and 2002b). 

In brief, the SeaBASS system consists of: (1)

the aforementioned data files, plus relevant

documentation and instrument calibration files,

(2) a directory tree structure used to house the

files, built on a dedicated server at NASA

Goddard Space Flight Center, and (3) a RDBMS

developed to further catalog, locate, and

distribute the files. Metadata from each data file

is stored in the RDBMS, and, as such, the

system may be queried to compile information

about the full bio-optical data set or to locate

specific data.

Through the use of online Common Gateway

Interface (CGI) forms that interface with the

RDBMS, the full bio-optical data set is

queriable and available to authorized users via

the World Wide Web. As of August 2002, all

data collected prior to 31 December 1999 are

available to the general public. A username and
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Figure 1.1 A map of the affiliations of SeaBASS data contributors (stars) and of relevant coastal

and island CIMEL stations (circles).

Figure 1.2 A map of all data points in the SeaBASS bio-optical data set.
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Figure 1.3 Maps of the distributions of common data parameters included in the bio-optical data

set. From top to bottom, the maps include (1) chlorophyll a concentrations (CHL), (2)

measurements of apparent optical properties (AOP), made using above water and profiling

radiometers, and (3) measurements of inherent optical properties (IOP), made using absorption

meters, backscattering sensors, and spectrophotometers.
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password are required to access the remaining

restricted data.

Historically, the data archived in SeaBASS

have predominantly been used for satellite-dataproduct validation activities (Figure 1.5) and

bio-optical algorithm development (OGReilly et

al. 1998, Bailey et al. 2000, Hooker and

McClain 2000, Moore et al. 2001, Maritorena et

al. 2002, Schwarz et al. 2002). As the number

of viable satellite ocean-color data sets has

increased, and the size and range of the

community has grown, however, these data have

also been used, by the SPO, for example, in

support of international protocol workshops,

data merger studies, and time series analyses.

In addition, all data collected prior to 31

December 1999 were submitted to the National

Oceanic and Atmospheric Administration

(NOAA) National Oceanic Data Center

(NODC) for inclusion in their national archive.

The development of a CD-ROM version of the

full public bio-optical and atmospheric data set

is planned for Fall 2002.

1.3 Report overview

The second chapter of this report describes

the current SeaBASS data submission and

access policies, including regulations for data

distribution and acknowledgment. In this

chapter, eligibility for accessing restricted data

is also discussed and the schedule for making

data public is outlined. In the third chapter, the

format of SeaBASS data files is fully described.

The fourth chapter outlines how a contributor

verifies the format of their files and submits

their data to SeaBASS. This chapter also

describes how the SeaBASS Administrator

verifies the format of a data file and evaluates

the data within. The fifth chapter summarizes

the architecture of the SeaBASS archive and its

RDBMS. It also illustrates how data are stored

and begins to describe how data are made

available to the user community. Finally, in the

sixth chapter, methods for accessing the biooptical data set via the World Wide Web are

presented in detail. In addition, supplementary

online utilities are described in this chapter. 

Figure 1.4 A map of all data points in the SeaBASS atmospheric data set. The locations of

MicroTops sun photometer data are indicated with stars, SIMBAD radiometer data with circles, and

FRSR data with single points.
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Figure 1.5 A representative example of standard output from the SPOAs satellite data product

validation activities. Specifically, in situ water-leaving radiances collected as part of the eighth

Atlantic Meridional Transect (AMT-8) campaign (May - June 1999), are compared with coincident

SeaWiFS data values.
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Chapter 2

SeaBASS Data and Access Policies

2.1 Introduction

The SeaBASS data policies outlined in this

report (and its references) apply to all data

collected under the NASA Ocean

Biogeochemistry Program at Goddard Space

Flight Center for inclusion in the calibration and

validation data set archived in SeaBASS. This

includes all data submitted to the SPO and

biological data collected under the NRA Ocean,

Ice, and Climate, released in October 2001.

Members of the SIMBIOS Science Team and

those receiving funding under the Ocean

Biogeochemistry Program must, at a minimum,

comply with this data policy, although the SPO

encourages a more open policy. Full detail on

the scope and extent of all SeaBASS data and

access policies is provided in the SIMBIOS

NRA-99-OES-99, Appendix B and in Firestone

and Hooker (2001). In addition, the details

included in this report are available online via

the SeaBASS World Wide Web site at:

<http://seabass.gsfc.nasa.gov/seabass_access.html>.

2.2 Data submission

Bio-optical algorithm development is

observation limited, and, therefore, rapid

turnaround and access to in situ data are

fundamental to advance the field of ocean color.

Principal Investigators (PIXs) supported by

SIMBIOS NRA-99-OES-09 contracts must

submit data within six months of its collection.

Data collected under funding from the NASA

Ocean Biogeochemistry Program must be

submitted within one year. International

Science Team members and those involved with

international ocean color missions, while not

required to do so, are also encouraged to

provide data to SeaBASS to foster additional

collaboration.

2.3 Data access

Data archived in SeaBASS fall under one of

two access categories, restricted or public. The

former includes the full bio-optical data set.

The latter excludes the most recently collected

data. To protect the publication rights of

contributorsX data, restricted access is granted

only to members of the SIMBIOS Science Team

and other individuals approved on a case-bycase basis, as agreed upon by the SPO. The

latter includes other NASA-funded researchers,

international Science Team members, and

regular voluntary contributors to the data

archive. Other investigators are able to query

for generic information about the restricted data,

such as, PI's, data parameters, and temporal and

spatial boundaries, but will be referred to the

contributors for access to the data itself.

At the three-year anniversary of their

collection, data are no longer restricted and are

made available to the general public. Data

contributors, however, may declare their data

available for public access at any time prior to

the three-year collection anniversary. As of

August 2002, all data collected prior to 31

December 1999 are available to the public.

These data have been released to the NODC and

are available via their Web site at:

<http://www.nodc.noaa.gov/col/projects/access/seabass.html>.

A courtesy citation, naming the contributor and

funding agency, accompanied these data.

The SPO will release additional data every

three years at the conclusion of each SIMBIOS

NRA. On occasion, special data sets for

algorithm development will be made available

to the research community without restrictions

with the approval of the SIMBIOS Science

Team.
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2.3.1 Restricted access

The following individuals are eligible for

access to the full bio-optical data set: (1) active

PIGs of the current SIMBIOS Science Team (i.e.,

those receiving funding under NRA-99-OES99); (2) members of affiliated NASA-sponsored

research programs or Science Teams, for

example, MODIS Terra and Aqua; (3) members

of international space agencies and associated

Science Team members who are regularly

contributing ocean color products to the SPO;

and (4) regular, voluntary, contributors of in situ

data, granted access on a case-by-case basis.

With regards to the latter, periodic and

substantial submission of in situ data is required

for consideration, and renewal of this status is

reviewed annually. An online application for

full access to SeaBASS is available at:

<http://seabass.gsfc.nasa.gov/cgi-bin/register_seabass.cgi>.

Applicants are required to provide their

affiliation, some general contact information,

and the local Internet Protocol (IP) addresses

from which they wish to access SeaBASS.

Specific usernames and passwords are normally

provided by the applicant, but will be generated

by the SeaBASS Administrator upon request.

Each PI is eligible for a single account and a

limited number of IP addresses from which

SeaBASS may be accessed. The number of IP

addresses allowed per PI is defined as two for

funded SIMBIOS or NASA-sponsored Science

Team members, and between three and five per

international PI or space agency. The latter is

determined at the discretion of the SPO and

typically depends on the size of the organization

and number of co-PIGs named in the SIMBIOS

proposal.

Each US and international PI is responsible

for applying for access to SeaBASS, distributing

their login information to the appropriate

members of their staff and co-PIGs, and

informing the SeaBASS Administrator of all IP

address and staffing changes. Likewise, the

calibration / validation manager, or appropriate

manager, of each space agency is responsible

for the above, but also accepts responsibility for

providing the SPO a list of all staff that will be

accessing SeaBASS. The SeaBASS

Administrator reserves the right to monitor all

accounts, IP addresses, and passwords, and may

implement additional security measures, as

necessary.

2.3.2 Public access

Users without restricted access privileges

who wish to access the public bio-optical data

set may do so freely, but are prompted to log in

each time they visit an online site where data

may be accessed. The information obtained at

this step is used only for statistical purposes and

to determine visitorsG interests, with the goal of

providing better service. For additional

information, read the NASA Website Privacy

Statement, provided at:

<http://webmaster.gsfc.nasa.gov/policy/gsfc/privacy.html>.

Occasionally, this information will be provided

to data contributors, upon request.

2.4 Distribution & acknowledgements

All users who are incorporating SeaBASS

data into their research are expected to

acknowledge both the data contributor and the

funding agency, either the NASA SIMBIOS or

SeaWiFS Project, or the NASA Ocean

Biogeochemistry Program, as appropriate

(Table 2.1). A citation should also be made of

the SeaBASS data archive. For restricted data,

the contributors have the right to be named as

co-authors, and users are encouraged to discuss

relevant findings with the contributor early in

their research. All users are required to provide

the contributors of data they are using a copy of

any manuscript prior to initial submission for

publication, thus presenting the contributor an

opportunity to comment on the paper.

Restricted data accessed from SeaBASS are

not to be distributed to unauthorized users. All

users and contributors are required to report

possible data errors and mislabels to the

SeaBASS Administrator. All questions
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regarding data, however, should be addressed to

the original data contributor and not to the

Administrator. The SPO will not be held

responsible for any data errors or misuse.

Table 2.1 Funded US SIMBIOS (under NRA-96-MTPE-04 and NRA-99-OES-99) and SeaWiFS

PI's who have contributed to the SeaBASS bio-optical data set, as of August 2002.

Principal Investigator Affiliation Funding Agency

Robert Arnone Naval Research Laboratory NASA SIMBIOS

William Balch Bigelow Laboratory for Ocean Sciences NASA SIMBIOS

John Brock United States Geological Survey NASA SIMBIOS

Chris Brown NOAA NASA SIMBIOS

Douglas Capone University of Maryland NASA SIMBIOS

Kendall Carder University of South Florida NASA SIMBIOS

Francisco Chavez Monterey Bay Aquarium and Research Institute NASA SIMBIOS

Glenn Cota Old Dominion University NASA SIMBIOS

Tom Dickey University of California, Santa Barbara NASA SIMBIOS

David Eslinger University of Alaska Y Fairbanks NASA SIMBIOS

Piotr Flatau Scripps Institute of Oceanography, University of California,

San Diego NASA SIMBIOS

Robert Frouin Scripps Institute of Oceanography, University of California,

San Diego NASA SIMBIOS

Lawrence Harding University of Maryland NASA SIMBIOS

Stanford Hooker NASA Goddard Space Flight Center NASA SeaWiFS,

NASA SIMBIOS

Mark Miller Brookhaven National Laboratory NASA SIMBIOS

Greg Mitchell Scripps Institute of Oceanography, University of California,

San Diego NASA SIMBIOS

Ru Morrison Woods Hole Oceanographic Institute, Massachusetts

Institute of Technology NASA SIMBIOS

James Mueller Center for Hydro-Optics and Remote Sensing, San Diego

State University NASA SIMBIOS

Frank Muller-Karger University of South Florida NASA SIMBIOS

Norman Nelson University of California, Santa Barbara NASA SIMBIOS

John Porter University of Hawaii NASA SIMBIOS

David Siegel University of California, Santa Barbara NASA SIMBIOS

James Spinhirne NASA Goddard Space Flight Center NASA SIMBIOS

Rick Stumpf NOAA Center for Coastal Monitoring and Assessment NASA SIMBIOS

Ajit Subramaniam University of Maryland NASA SIMBIOS

Ronald Zaneveld Oregon State University NASA SIMBIOS
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Chapter 3

The SeaBASS Data File Format

3.1 Overview

The design of a SeaBASS data file was

conceived based on a need for effortless data

access, including online access, while

accommodating a variety of computer operating

systems. The objective was a simple and logical

format that was easily expandable, portable

across all computer platforms, web accessible,

and manageable using a RDBMS. Accordingly,

all SeaBASS data files are currently flat, twodimensional text files that adhere to the basic

American Standard Code for Information

Interchange (ASCII) format. The SPO believes

that the basic ASCII format most readily

satisfies the prerequisite conditions, while also

being the most approachable format by the

widest user audience.

The format was further designed to be selfdescribing. Each file is comprised of two parts,

a header block followed by a data block (Figure

3.1). The former consists of a series of

keywords and values intended to provide

descriptive information about the data in the

file, for example, the source of the data and its

spatial and temporal limits. The latter contains

a matrix of data values, similar to the

organization of a spreadsheet. File names are

not required to follow any specific naming

convention, rather, they are left the discretion of

the data contributors

3.2 The header block

The keyword-based approach was

implemented to enhance automated processing,

as the standard vocabulary permits data files to

be easily parsed. Each keyword and its

argument in the header block occupy one line in

the block. The format is:

/keyword=value,

where keyword is an approved, case-insensitive

keyword (Table 3.1) that must begin with a

slash (/) and value is a string or number which

assigns value to the keyword. The exceptions

are /begin_header and /end_header, which

do not have input arguments.

Every data file opens with /begin_header.

The headers may then be listed in any order, so

long as the list ends with /end_header.

Commas separate multiple arguments for a

given keyword, for example, in the case of

multiple data contributors:

/investigator=John_Smith,Mary_Jones.

White space (blanks) and apostrophes (T),

however, are invalid characters. Underscores

are used to separate words, as indicated in the

above example. For those keywords accepting

numeric arguments, specific data units are

required, as noted in Table 3.1.

In general, the International System of Units

(SI) is used, except where traditional usage

dictates otherwise. Units are not listed in the

header block, with the exception of those

keywords relating to time and location, for

example, /start_time and /north_latitude,

which require additional notation in the form of:

/keyword=value[units],

where [units] is set equal to V[GMT]Z or

V[DEG]Z, respectively, indicating units of

Greenwich Mean Time (GMT) and decimal

degrees.

Header keywords are divided into two

groups, those required in every data file, and

those used to provide additional, optional,

information about the data in the file. A value

of VNAZ (Vnot availableZ or Vnot applicableZ)

may be assigned to any keyword where

information cannot be provided. Data files with

missing required headers will not be accepted

for submission to SeaBASS. 
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Figure 3.1 The basic SeaBASS data file structure. Each file includes of two parts, a header block,

which contains descriptive information about the file and its data, and a data block, which consists

of a matrix of geophysical values.

Table 3.1. SeaBASS metadata headers, as of August 2002. (A previous version of this table was

originally published in Werdell et al. (2002a)).

Header Required Description

/begin_header Y The first line of every data file, indicating the beginning of the header

block. This header does not have an input argument.

/investigators Y The name of the principal investigator, followed by any associate

investigators.

/affiliations Y A list of affiliations, e.g., university and laboratory, for each investigator.

/contact Y An electronic mail address for at least one of the investigators or point of

contact for the data file.

/experiment Y The name of the long-term research project, e.g., CalCOFI and CARIACO.

An entry of NSIMBIOSP is not permitted.

/cruise Y

The name of the specific cruise, or subset of the experiment, where the data

in the file were collected e.g., cal9802 and car48. An entry of NSIMBIOSP is

not permitted.

/station N The name of the station or deployment area where data in the file were

collected.

/data_file_name Y The current name of the data file.
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/documents Y

A list of cruise reports, station logs, digital images, and other associated

documentation which provide additional information about the experiment

and cruise. This documentation must accompany the data file at the time of

submission.

/calibration_files Y

A list of supplementary files containing coefficients and techniques used to

calibrate the instruments used in data collection. This documentation must

accompany the data files at the time of submission.

/data_type Y

The general collection method, platform, or type of data found in the file.

Acceptable values include: cast for vertical profiles, e.g., optical packages

and CTD; flow_thru for continuous data, e.g., shipboard and underway

flow through systems; above_water for above surface radiometry data, e.g.,

ASD, SIMBAD, and Satlantic SAS; sunphoto for sun photometry data,

e.g., MicroTops and PREDE; mooring for moored and buoy data; drifter

for drifter and drogue data; scan for discrete hyperspectral measurements;

lidar for lidar and other active remote-sensing measurements, e.g., MPL;

and pigment for laboratory measured pigment data, e.g., fluorometry and

HPLC.

/data_status N

The condition, or status, of the data file. The value preliminary indicates

the data are new and the investigator intends to analyze the data further. The

value update indicates the data are being resubmitted and informs the SPO

that a resubmission will occur in the future. The value final indicates the

investigator has no intention of revisiting the data set.

/start_date Y The earliest date data in the file were collected, in the form YYYYMMDD.

/end_date Y The latest date data in the file were collected, in the form YYYYMMDD.

/start_time Y

The earliest time of day data in the file were collected, in the form

HH:MM:SS. Values are required to be in GMT. This header requires a

[GMT] trailer, e.g., /start_time=02:45:30[GMT].

/end_time Y

The latest time of data in the file were collected, in the form HH:MM:SS.

Values are required to be in GMT. This header requires a [GMT] trailer,

e.g., /end_time=02:56:20[GMT].

/north_latitude Y

The farthest north data in the file were collected, in decimal degrees. This

header requires a [DEG] trailer, e.g., /north_latitude=45.223[DEG].

Coordinates south of the equator are set negative.

/south_latitude Y

The farthest south data in the file were collected, in decimal degrees. This

header requires a [DEG] trailer, e.g., /south_latitude=31.884[DEG].

Coordinates south of the equator are set negative.

/east_longitude Y

The farthest east data in the file were collected, in decimal degrees. This

header requires a [DEG] trailer, e.g., /east_longitude=170.225[DEG].

Coordinates set west of the Prime Meridian are set negative.

/west_longitude Y

The farthest west data in the file were collected, in decimal degrees. This

header requires a [DEG] trailer, e.g., /west_longitude=160.117[DEG].

Coordinates set west of the Prime Meridian are set negative.
The SeaWiFS Bio-Optical Archive and Storage System...

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/cloud_percent N Percent cloud cover for the entire sky, e.g., 0 for a cloud-free sky and 100

for a completely overcast sky.

/measurement_depth N

The discrete depth at which data were collected, in meters. This header is

required for bottle samples, shipboard flow-through systems, buoys, and

moored radiometers.

/secchi_depth N The secchi depth at the station where the data were collected, in meters.

/water_depth Y The water depth at the station where the data were collected, in meters.

/wave_height N The wave height at the station where the data were collected, in meters.

/wind_speed N The wind speed at the station where the data were collected, in meters per

second.

! COMMENTS N

A space for additional comments. Common comments include additional

ancillary information about the data file, sea and sky states, difficulties

encountered during data collection, methods of data collection, instruments

used, and a description of nonstandard SeaBASS field names included in

the data file.

/missing Y

The null value used as a numeric placeholder for any missing data in the

data file. Each row of data must contain the same number of columns as

defined in the /fields and /units headers. Only one missing value is

allowed per file. It is required that this value be non-zero.

/delimiter Y The delimiter of the columns of data. Accepted delimiters include tab,

space, and comma. Only a single delimiter is permitted per data file.

/fields Y

A list of the fields, e.g., CHL, for each column of data included in the data

file. Each entry describes the data in a single column, and every column

must have an entry.

/units Y

A list of the units, e.g., mg m-3, for each column of data included in the data

file. Every value in /fields must have an appropriate value listed in this

header.

/end_header Y The final line of the header block, indicating the beginning of the data

block. This header does not have an input argument.

Additional notation and information may be

incorporated at any time in the header block as

comment lines, which begin with an

exclamation point (!). Unlike the keyword

entries, comment lines are not restricted in

format and may include both white spaces and

apostrophes. An online description of each

header keyword and its expected argument is

available on the SeaBASS Web page at:

<http://seabass.gsfc.nasa.gov/seabass_header.html>.

3.3 Standard field names

The /fields and /units headers identify

every column in the data block. Every value in

the /fields header names a column in the data

block, for example, YCHLZ, and every value in

the /units header provides units for that

column, for example, Ymg m-3Z. Fields and

units are listed in the order the data are provided

in the data block. Each column is required to

have a corresponding /fields and /units

entry; as such, the number of entries in the

/fields and /units headers and the number of

columns in the data block must be equal.

To ensure compatibility within the data

archive, a standard set of case-insensitive field

names and units has been adopted (Table 3.2).

While the list is reasonably comprehensive, it

does not account for all of the data types one

might wish to provide to the archive. Data types
The SeaWiFS Bio-Optical Archive and Storage System...

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Table 3.2 The SeaBASS standardized parameters, with their appropriate abbreviations, units, and

descriptions, as of August 2002. The notation ###.# indicates the parameter is wavelength specific,

in nanometers, with the form of, for example, 490.6. The parameter abbreviations shown are

mandated by the standard SeaBASS data file format. There are some limitations imposed on the

format of the abbreviation because ASCII text is used, as described in the Section 3.3. (A previous

version of this table was originally published in Werdell et al. (2002a)).

Abbreviation Unit Abbreviation Description

a###.# m-1 Total absorption coefficient

aaer###.# m-1 Absorption coefficient of atmospheric aerosols

ad###.# m-1 Absorption coefficient of detritus

adg###.# m-1 Absorption coefficient of detritus plus CDOM

ag###.# m-1 Absorption coefficient of CDOM

agp###.# m-1 Absorption coefficient of CDOM plus particles

altitude m Altitude above sea level

am unitless Air mass

angstrom unitless Ångström exponent

AOT###.# unitless Aerosol optical thickness

ap###.# m-1 Absorption coefficient of particles

aph###.# m-1 Absorption coefficient of phytoplankton

a*ph###.# m-1 Chlorophyll a-specific absorption coefficient of phytoplankton

At degrees C Air temperature

b###.# m-1 Total scattering coefficient

bb###.# m-1 Backscatter coefficient

bincount none Number of records averaged into a bin

bnw###.# m-1 Total scattering coefficient minus the scattering by water

bp###.# m-1 Particle scattering coefficient

c###.# m-1 Beam attenuation coefficient

cloud % Percent cloud cover

cnw###.# m-1 Beam attenuation coefficient minus the scattering by water

cond mmho cm-1 Conductivity

date yyyymmdd Sample date

day dd Sample day

depth m-1 Depth of measurement

Ed###.# uW cm-2 nm-1 Downwelling irradiance

EdGND Volts Dark current values for Ed sensor

Elw uW cm-2 Downwelling irradiance over the infrared spectrum, 3 to 40 m

Epar uE cm-2 s-1 ♦ Profiled PAR

Es###.# uW cm-2 nm-1 Downwelling irradiance above the surface

EsGND volts Dark current values for Es sensor

Esky###.# uW cm-2 nm-1 Downwelling sky irradiance

Esun###.# uW cm-2 nm-1 Downwelling direct normal sun irradiance

Esw uW cm-2 Downwelling irradiance over the solar spectrum, 0.3 to 3 m

Eu###.# uW cm-2 nm-1 Upwelling irradiance

EuGND volts Dark current values for Eu sensor

F0###.# uW cm-2 nm-1 Extraterrestrial solar irradiance

hour hh Sample hour

It degrees C Instrument temperature

 

 The unit [mmho\ (the so-called [milli-mho\) is the traditional unit used in conductivity studies. In SI units, it is

equivalent to the reciprocal of the ohm (or the siemens).

♦ The unit E, for Einstein, is the traditional unit used in PAR studies. In SI units, it is equivalent to 1 mole quanta, or 1

mole photons.
The SeaWiFS Bio-Optical Archive and Storage System...

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jd jjj Sequential day of year

Kd###.# m-1 Diffuse attenuation coefficient of downwelling irradiance

Kl###.# m-1 Diffuse attenuation coefficient of upwelling radiance

Knf###.# m-1 Diffuse attenuation coefficient of natural fluorescence of chlorophyll a

Kpar m-1 Diffuse attenuation coefficient of PAR

Ku###.# m-1 Diffuse attenuation coefficient of upwelling irradiance

lat degrees Sample latitude

lon degrees Sample longitude

Lsky###.# uW cm-2 nm-1 sr-1 Sky radiance

Lt###.# uW cm-2 nm-1 sr-1 Total water radiance

Lu###.# uW cm-2 nm-1 sr-1 Upwelling radiance

LuGND volts Dark current values for Lu sensor

Lw###.# uW cm-2 nm-1 sr-1 Water-leaving radiance

Lwn###.# uW cm-2 nm-1 sr-1 Normalized water-leaving radiance (LWN = LW F0 /Es)

minute mn Sample minute

month mo Sample month

natf nE m-2 sr-1 s-1 Natural fluorescence of chlorophyll a

nrb photoelectrons

 s

-1 shot-1 Normalized relative backscatter

Oz Dobson units Column ozone

PAR uE cm-2 s

-1 PAR measured at the sea surface

pitch degrees Instrument pitch

PP mg C/mg chla/h♠ Primary productivity

pressure dbar Water pressure

pressure_atm mbar Atmospheric pressure

Q###.# sr Eu /Lu (equal to π in diffuse water)

quality none Analyst-defined data quality flag

R###.# unitless Irradiance reflectance (R = Eu /Ed)

RelAz degrees Sensor azimuth angle relative to the solar plane

Rl###.# sr R1 Radiance reflectance (RL = Lu /Ed)

roll degrees Instrument roll

Rpi###.# unitless Radiance reflectance with π

Rrs###.# sr R1 Remote-sensing reflectance (Rrs = LW /Es)

sal PSU Salinity

sample none Sample number

SAZ degrees Solar azimuth angle

second ss Sample second

SenZ degrees Sensor zenith angle

sigmaT kg m-3 Density R 1000 kg m-3

sigma_theta kg m-3 Potential density R 1000 kg m-3

SN none Instrument serial number

SPM g L-1 Total suspended particulate material

SST degrees C Sea surface temperature

station none Sample station

stimf volts Stimulated fluorescence of chlorophyll a

SZ m Secchi disk depth

SZA degrees Solar zenith angle

tilt degrees Instrument tilt

time hh:mm:ss Sample time

trans % Percent transmission

volfilt L Volume filtered

waveheight m Wave height

 

♠ This parameter has the units of Ymilligrams of carbon per milligrams of chlorophyll a per hourZ. The individual units

are separated with the solids (/), instead of the customary reciprocals, to avoid confusion as to how it is to be formatted.
The SeaWiFS Bio-Optical Archive and Storage System...

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wavelength nm Wavelength of measurement

windspeed m s-1 Wind speed

Wt degreesC Water temperature

Wvp mm Water vapor

year yyyy Sample year

 Pigments:

Allo mg m-3 HPLC alloxanthin

Anth mg m-3 HPLC antheraxanthin

Asta mg m-3 HPLC astaxanthin

Beta-beta-Car mg m-3 HPLC ββ-carotene (β-carotene)

Beta-epi-Car mg m-3 HPLC βε-carotene (α-carotene)

Beta-psi-Car mg m-3 HPLC βψ -carotene (γ-carotene)

But-fuco mg m-3 HPLC 19'-butaonoyloxyfucoxanthin

Cantha mg m-3 HPLC canthaxanthin

CHL mg m-3 Fluorometrically or spectrophotometrically-derived chlorophyll a

Chl_a mg m-3 HPLC chlorophyll a

Chl_a_allom mg m-3 HPLC chlorophyll a allomers

Chl_a_prime mg m-3 HPLC chlorophyll a epimer

Chl_b mg m-3 HPLC chlorophyll b

Chl_c mg m-3 HPLC chlorophyll c

Chl_c1c2 mg m-3 HPLC chlorophyll c1 and c2

Chl_c3 mg m-3 HPLC chlorophyll c3

Chlide_a mg m-3 HPLC chlorophyllide a

Chlide_b mg m-3 HPLC chlorophyllide b

Croco mg m-3 HPLC crocoxanthin

Diadchr mg m-3 HPLC diadinochrome

Diadino mg m-3 HPLC diadinoxanthin

Diato mg m-3 HPLC diatoxanthin

Dino mg m-3 HPLC dinoxanthin

DV_Chl_a mg m-3 HPLC divinyl chlorophyll a

DV_Chl_b mg m-3 HPLC divinyl chlorophyll b

Echin mg m-3 HPLC echinenone

epi-epi-Car mg m-3 HPLC εε-carotene (ε-carotene)

Et-8-carot mg m-3 HPLC ethyl-apo-8'-carotene

Et-chlide_a mg m-3 HPLC ethyl chlorophyllide a

Et-chlide_b mg m-3 HPLC ethyl chlorophyllide b

Fuco mg m-3 HPLC fucoxanthin

Hex-fuco mg m-3 HPLC 19'-hexanoyloxyfucoxanthin

Lut mg m-3 HPLC lutein

Lyco mg m-3 HPLC lycopene

Me-chlide_a mg m-3 HPLC methyl chlorophyllide a

Me-chlide_b mg m-3 HPLC methyl chlorophyllide b

MV_Chl_a mg m-3 HPLC monovinyl chlorophyll a

MV_Chl_b mg m-3 HPLC monovinyl chlorophyll b

Mg_DVP mg m-3 HPLC Mg 2,4-divinyl phaeoporphyrin a5 monomethyl ester

Monado mg m-3 HPLC monadoxanthin

Neo mg m-3 HPLC neoxanthin

P-457 mg m-3 HPLC P-457

Perid mg m-3 HPLC peridinin

PHAEO mg m-3 Total phaeopigment concentration

Phide_a mg m-3 HPLC phaeophorbide a

Phide_b mg m-3 HPLC phaeophorbide b

Phide_c mg m-3 HPLC phaeophorbide c

Phythl-chl_c mg m-3 HPLC phytylated chlorophyll c
The SeaWiFS Bio-Optical Archive and Storage System...

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Phytin_a mg m-3 HPLC phaeophytin a

Phytin_b mg m-3 HPLC phaeophytin b

Phytin_c mg m-3 HPLC phaeophytin c

Pras mg m-3 HPLC prasinoxanthin

Pyrophytin_a mg m-3 HPLC pyrophaeophytin a

Pyrophytin_b mg m-3 HPLC pyrophaeophytin b

Pyrophytin_c mg m-3 HPLC pyropheophytin c

Siphn mg m-3 HPLC siphonein

Siphx mg m-3 HPLC siphonaxanthin

Tot_Chl_a mg m-3 HPLC divinyl chlorophyll a plus monovinyl chlorophyll a plus

chlorophyllide a plus chlorophyll a allomers plus chlorophyll a epimer

Tpg mg m-3 Total pigment concentration

Vauch mg m-3 HPLC vaucheriaxanthin-ester

Viola mg m-3 HPLC violaxanthin

Zea mg m-3 HPLC zeaxanthin

that do not fall under one of the predefined

standard field names may be included in a

submitted data file. The contributor, however,

is asked to define each non-standard data type as

a comment in the header block. If there are

frequent queries for non-standard data types,

then the new field names and associated units

will be included in the standard list. An online,

regularly updated, version of the standard field

names list is available via the SeaBASS Web

page at:

<http://seabass.gsfc.nasa.gov/cgi-bin/stdfields.cgi>.

Note that data values are required to be in

meaningful geophysical units (e.g., providing

voltages with conversion coefficients is

unacceptable). Note also that there are some

limitations and restrictions imposed on the

format of the unit abbreviations because ASCII

text is used. For example, although Tper meterU

is classically represented as Tm-1U, the format to

input would be Tm-1U or T1/mU, the latter being

the reciprocal of the unit. In addition, the letter

TuU is used in the unit abbreviations (e.g., TuW

cm-2 nm-1U) instead of the Greek letter μ,

again, because Greek letters cannot be used in

an ASCII file.

Whenever possible, the standard field names

and units assigned to each data parameter were

specified based on traditional oceanographic

and atmospheric abbreviations as listed in

current literature. The standard names assigned

to high performance liquid chromatography

(HPLC) derived pigments are based on

abbreviations defined by the Scientific

Committee on Oceanic Research (SCOR)

Working Group 78, as listed in Jeffrey et al.

(1997).

3.4 The data block

In the data block, values are provided as a

matrix (i.e., in columns), similar to a

spreadsheet. Spaces, tabs, or commas may be

used to delimit each column, provided a single,

consistent delimiter is used throughout the data

file and its appropriate value is listed in the

/delimiter header. Each row of data is

terminated with a carriage return. Data that are

missing, bad, or unavailable are replaced with a

numeric blank, for example, T-999U, whose

value is non-zero and a non-observable value

for the particular data type. Only a single

numeric blank may be used per file and this

value must be listed in the /missing header.

Exponential notation is acceptable, in the form:

<n>e<x>, where <n> is a numeric entry and

<x> is the exponential value, for example,

T3.33e-4U. Latitude and longitude are provided

in decimal degrees, with coordinates north of

the equator and east of the Prime Meridian set

positive. Water depth and pressure values are

listed as increasing positive with increasing

depth.

Each file should be segmented into a logical

grouping, such as, by station, date, or parameter,

or based on the measurement or instrument type.
The SeaWiFS Bio-Optical Archive and Storage System...

18

For example, all parameters collected in a single

depth profile or spectrophotometric analysis of a

discrete water sample should be incorporated

into a single data file (Figures 3.2 and 3.3). On

the contrary, multiple discrete measurements

collected at several stations may be incorporated

into a single file (Figure 3.4), provided the

appropriate metadata (e.g., date, time, latitude,

longitude, depth, and station) are also included

as data columns.

/begin_header

/investigators=John_Smith,Mary_Johnson

/affiliations=MBARI,State_University

/contact=jsmith@mbari.org,mary@state.edu

/experiment=TAO_Moorings

/cruise=gp1-02-ka

/station=341

/data_file_name=cast_example.txt

/documents=TAO_README.txt

/calibration_files=ocp14a.cal

/data_type=cast

/data_status=preliminary

/start_date=19971215

/end_date=19971215

/start_time=21:15:39[GMT]

/end_time=21:19:30[GMT]

/north_latitude=-0.016[DEG]

/south_latitude=-0.016[DEG]

/east_longitude=-170.02[DEG]

/west_longitude=-170.02[DEG]

/cloud_percent=10.0

/measurement_depth=NA

/secchi_depth=NA

/water_depth=2100

/wave_height=0.5

/wind_speed=5

!

! Downcast better than upcast.

!

/missing=-999

/delimiter=space

/fields=depth,Lu412.2,Lu443.4,Lu489.7,Lu510.0

/units=m,uW/cm^2/nm/sr,uW/cm^2/nm/sr,uW/cm^2/nm/sr,uW/cm^2/nm/sr

/end_header@

0.0 5.856900 5.989949 5.787405 4.898884 4.280903

1.0 1.244184 1.066594 0.852400 0.461248 0.177923

2.0 1.299710 1.113997 0.884608 0.457049 0.159074

3.0 1.298214 1.113140 0.886502 0.455522 0.155225

...

Figure 3.2 A representative example of a SeaBASS cast data file.
The SeaWiFS Bio-Optical Archive and Storage System...

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/begin_header

/investigators=Greg_Smith,Mary_Johnson

/affiliations=UCSD_SIO

/contact=gsmith@ucsd.edu

/experiment=CALCOFI

/cruise=CAL9910

/station=93.28

/data_file_name=scan_example.txt

/documents=README.cal9910

/calibration_files=cal9910_scanlog.txt

/data_type=scan

/data_status=final

/start_date=19991003

/end_date=19991003

/start_time=19:20:00[GMT]

/end_time=19:20:00[GMT]

/north_latitude=34.392[DEG]

/south_latitude=34.392[DEG]

/east_longitude=-124.327[DEG]

/west_longitude=-124.327[DEG]

/cloud_percent=20

/measurement_depth=10

/secchi_depth=22.1

/water_depth=230

/wave_height=1

/wind_speed=3.7

!

! Method of estimating particulate absorption:

! Mitchell, B.G., Ocean Optics X, p.137-148, 1990

!

! The spectral range is 400 nm - 750 nm with 2 nm step

!

/missing=-999

/delimiter=space

/fields=wavelength,ad,ap,ag

/units=nm,1/m,1/m,1/m

/end_header@

400 0.00533 0.01217 0.01162

402 0.00528 0.01246 0.02508

404 0.00525 0.01282 0.02931

406 0.00523 0.01323 0.02713

408 0.0052 0.01369 0.02098

410 0.00516 0.01416 0.01852

412 0.0051 0.0146 0.00693

414 0.00502 0.01502 0.01381

416 0.00492 0.01539 0.00973

418 0.00481 0.01572 0.0126

420 0.00469 0.01603 0.00691

...

Figure 3.3 A representative example of a SeaBASS scan data file.
The SeaWiFS Bio-Optical Archive and Storage System...

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/begin_header

/investigators=John_Smith,Mary_Johnson

/affiliations=Goddard_Space_Flight_Center,State_University

/contact=jsmith@simbios.gsfc.nasa.gov,mary@state.edu

/experiment=AMT

/cruise=AMT07

/station=NA

/data_file_name=chl_example.txt

/documents=A7OPSLOG.TXT

/calibration_files=A7CHL.cal

/data_type=pigment

/data_status=preliminary

/start_date=19981016

/end_date=19981016

/start_time=12:11:08[GMT]

/end_time=15:25:45[GMT]

/north_latitude=36.1234[DEG]

/south_latitude=31.8823[DEG]

/east_longitude=-51.2363[DEG]

/west_longitude=-55.1125[DEG]

/cloud_percent=NA

/measurement_depth=NA

/secchi_depth=NA

/water_depth=NA

/wave_height=NA

/wind_speed=NA

!

! Turner fluorometer last calibrated 27 Mar 2000 JMW

!

/missing=-999

/delimiter=space

/fields=date,time,station,lat,lon,depth,CHL

/units=yyyymmdd,hh:mm:ss,none,degrees,degrees,m,mg/m^3

/end_header@

19981016 14:33:22 st001 32.3234 -53.1624 0.5 0.32

19981017 13:01:56 st002 33.1122 -53.1276 0.5 0.33

19981018 15:25:45 st003 36.1234 -51.2363 0.5 0.45

19981019 12:11:08 st004 31.8823 -55.1125 0.5 0.22

19981020 14:13:14 st005 34.2341 -52.3545 0.5 0.11

...

Figure 3.4 A representative example of a SeaBASS pigment data file.
The SeaWiFS Bio-Optical Archive and Storage System...

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Chapter 4

Data Submission and Quality Control

4.1 Introduction

Both bio-optical algorithm development and

ocean color sensor validation analyses are

observation limited, and, therefore, access to

high quality in situ data is fundamental for their

progress. Accordingly, the SPO has defined a

series of standard oceanographic and

atmospheric parameters, instrument

specification and calibration techniques, field

measurement methods, and data submission

protocols to ensure that data archived in

SeaBASS would be acceptable for such

activities (Mueller et al. 2002a and 2002b).

While the latter requires a specific data file

format (as outlined in Chapter 3 of this report),

the data submission protocols were designed to

be as straightforward and effortless on the part

of the contributor, while still offering a useful

format for internal SPO efforts. This chapter

describes how data files are submitted to

SeaBASS and the path of these data through the

SeaBASS system (Figure 4.1).

4.2 FCHECK

The SPO developed feedback software to

evaluate the format of submitted data files, the

principal component of which is known as

FCHECK. FCHECK consists of Practical

Extraction and Report Language (PERL) code,

several lookup tables, and UNIX / LINUX mail

handling utilities. It evaluates the header and

data blocks of an input file by parsing each and

comparing the metadata and data with a series

of prerequisite criteria. The output (Figure 4.2)

is a series of warnings and errors, where

warnings are used to indicate that some

desirable condition was not met, for example, an

optional header was not provided, and each

error references a point where the file format is

invalid. With regards to the header block,

FCHECK verifies that the following conditions

are met:

• all required headers are provided;

• the /begin_header and /end_header

keywords are included;

• the arguments for the time keywords are in

the range and format 00:00:00 to 23:59:59;

• the arguments for the date keywords are in

the format YYYYMMDD, where YYYY is the

four-digit year, and MM and DD are the twodigit month and day, respectively;

• the arguments for the latitude keywords are

in the range and format ^90.0 to 90.0;

• the arguments for the longitude keywords are

in the range and format ^180.0 to 180.0;

• bracketed arguments, e.g., `[GMT]d, are

provided for each time and location keyword;

• the arguments for the /data_type and

/data_status keywords are recognized

options;

• the arguments for the /delimiter keyword

is a recognized option and applicable for the

data block;

• the /missing keyword has only one

argument;

• the number of /fields and /units

arguments are equal; and

• the associated /units argument is valid for

each standardized /fields argument.

For the data block, FCHECK verifies that the

following conditions are met:

• the number of columns in each row is equal

to the number of /fields and /units

arguments;

• all date and time data are within acceptable

ranges, e.g., hour values between 00 and 23;

• all location data are within acceptable ranges,

e.g., latitude values between ^90.0 and 90.0;

and
The SeaWiFS Bio-Optical Archive and Storage System...

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Figure 4.1 An illustrative example of how data files and documentation are handled after

their submission to SeaBASS.

• all other data are within reasonable ranges,

e.g., non-negative pigment concentrations.

FCHECK is made available to the

community using electronic mail and file

transfer protocol (FTP). The electronic mail

address for FCHECK is:

<fcheck@seabass.gsfc.nasa.gov>.

A contributor may evaluate a single file by

electronically mailing the data file to this

address. The simultaneous evaluation of

multiple data files requires several steps. First,

the contributor creates a new directory in the

SeaBASS FTP site at:

<ftp://samoa.gsfc.nasa.gov/seabass/fcheck>,

and uploads the files to be evaluated to this

directory. The contributor then sends electronic
The SeaWiFS Bio-Optical Archive and Storage System...

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FCHECK Ver. 3.0 last modified: Jul 26 2002 09:49:07

File: chl20020110_1400.sb

This file has passed the FCHECK program.

FCHECK Ver. 3.0 last modified: Jul 26 2002 09:49:07

File: iop20020110_1400.sb

This file has passed the FCHECK program but 1 warnings were issued.

*************************** WARNINGS: *******************************

1) Negative value detected in data block for field(s):

aph ap ad

FCHECK Ver. 3.0 last modified: Jul 26 2002 09:49:07

File: spmr20020110_1400.sb

This file has failed the FCHECK program.

2 errors were found.

**************************** ERRORS: ********************************

1) Missing value not allowed for depth!

2) Header /fields:

solar_time_gmt water_temp is(are) not found in the names

list at http://seabass.gsfc.nasa.gov/cgi-bin/stdfields.cgi

This may be due to one of the following:

a) The fieldname is incorrectly formatted [Lw_490 rather than

the required Lw490]

b) The fieldname is not typical for standard SeaBASS

submission, i.e. it's new to us! If the fieldname does not

have an equivalent standardized name, please contact the

SeaBASS administrator to discuss how to submit the information

Figure 4.2 Several examples of the standard output of FCHECK, the SeaBASS data file format

verification software. From top to bottom, the three evaluated files (1) fully passed FCHECK, (2)

passed FCHECK, but warnings were issued, and (3) failed to pass FCHECK.

mail to FCHECK with the specific subject line

LFTP: <new directory>Q where <new

directory> is the name of the directory created

in the first step. The receipt of this

electronic mail triggers FCHECK to evaluate

each file in <new directory>. For both methods

of invoking of FCHECK, the results of the

analyses are electronically mailed back to the

contributor and to the SeaBASS Administrator.

Additional help is available by sending

electronic mail to FCHECK with the word

LHELPQ in the subject line and via the

SeaBASS Web site.

4.3 Documentation

An often unspoken, yet underlying, objective

of the SPO is to maintain sufficient information

and detail about the archived data as to make the

full bio-optical set as complete as possible and,
The SeaWiFS Bio-Optical Archive and Storage System...

24

therefore, maximally approachable to an outside

user. The SPO feels that complete

documentation both reinforces accurate use of

the data and encourages future data corrections

and updates, when necessary. Further, complete

documentation enhances the preservation of

these data when submitted to the NODC. As

such, the SeaBASS Administrator will accept

any and all supporting documentation deemed

relevant by the data contributor.

At a minimum, the SPO requires that the

supporting documentation include two files, a

cruise report and an instrument report. The

format of the former is left to the discretion of

the contributor, so long as it includes a station

log that provides ancillary information or

comments for each measurement, such as date,

location, sea and sky states, and other

observations. Contributors are encouraged to

include additional documentation, such as

digital photographs of sea and sky states. The

latter should be either a report that lists the

instruments used and the data processing

methods, equations, and any relevant references,

or the instrument calibration files themselves.

Calibration files must include both calibration

coefficients and the date each instrument was

calibrated. In cases where this information is

not available or relevant per se, a brief

document describing any calibration techniques

or reasons for the former is acceptable.

4.4 Data submission

Data files and supporting documentation are

submitted to SeaBASS via FTP. Note that using

the FTP version of FCHECK does not constitute

a submission to SeaBASS. Once a data

contributor has finished preparing their data

files, and each of these files have passed

FCHECK, both the data files and the supporting

documentation and instrument calibration files

are uploaded to the SeaBASS FTP site at:

<ftp://samoa.gsfc.nasa.gov/seabass/incoming>.

The data contributor will need to create a

unique directory for their data, if one does not

already exist. Once the data are uploaded, the

data contributor is asked to inform the SeaBASS

Administrator via electronic mail that data have

been submitted. As described in Chapter 2, all

US SIMBIOS Science Team members and

researchers receiving funding under the Ocean,

Ice, and Climate NRA are obligated to submit

data within six months and one year,

respectively, of its collection.

4.5 Evaluation of data file formats

The SeaBASS Administrator routinely

collects data uploaded to the FTP site. Prior to

ingestion into the data archive, however, the

submission and the data filesU format are

evaluated using several standard quality control

(QC) procedures. First, the submission is

inspected for completeness. All available

supporting documentation and instrument

calibration files must accompany the submitted

data files. These files must match exactly the

arguments listed for the /documents and

/calibration_files header keywords. 

Submissions that do not include supporting

documentation and calibration files are

considered incomplete and the data files will not

be archived. Next, the format of each file is

evaluated using FCHECK. The Administrator

will occasionally waive certain reported errors,

if unavoidable for a given file or data type.

Otherwise, the data contributor must address

and resolve all errors reported by FCHECK.

Once a data file has passed FCHECK, its

header block is further evaluated with the

following guidelines. The arguments for the

/experiment and /cruise keywords must be

consistent amongst all files in the submission

and all previously submitted data from the

specific cruise. The arguments for the

/data_type and /data_status keywords must

be valid, for example, either YpreliminaryZ,

YupdateZ, or YfinalZ for /data_status, and

accurate. Certain optional headers must be

present for specific data types for which they

provide relevant information, such as, the

keyword /measurement_depth for

spectrophotometric analyses of discrete water

samples. And, the single argument for the

/missing header must be numeric and a non-
The SeaWiFS Bio-Optical Archive and Storage System...

25

valid data value for the given data type. 

Additionally, all white space is removed from

the header block, with the exception of any

comment lines, and all non-standard field names

must be defined as a comment line in each file

in which they are used. With regards to both the

header and data blocks, the date, time, latitude,

and longitude data values reported in each file

must be within an acceptable range, for

example, ±90 for latitude.

The Administrator regularly creates a map of

data points for each specific cruise to verify that

the data are reasonably continuous and oceanic

(Figure 4.3). All missing values in both blocks

are located and verified. Finally, the

Administrator adds one or two additional pieces

of information to each data file. An additional

header keyword and argument,

/received=YYYYMMDD, is added to each file to

document the date of submission of the data file.

For the header argument, YYYY is the four-digit

year, MM is the two-digit month, and DD is the

two-digit day. And, comment lines describing

changes are added to any data file whose

content was modified by the Administrator.

4.6 Evaluation of data

The SPO has developed an additional series

of QC protocols, and accompanying software, to

assist in evaluating the quality of submitted

radiometric data and to prepare the data for

various satellite-validation activities. These

practices were developed to further aid in (1)

verifying the radiometric accuracy of the in situ

data, (2) evaluating the radiometric stability of

the field instruments, particularly for long term

time series submitted to SeaBASS, and (3)

developing consistency amongst the data used to

validate the satellite-derived data products.

Figure 4.3 A regional map generated by the SeaBASS Administrator to verify the accuracy of the

location coordinates provided in a series of submitted SeaBASS data files.
The SeaWiFS Bio-Optical Archive and Storage System...

26

Figure 4.4 A screen-capture of the interactive software, Visual SeaBASS, used by the SPO to

evaluate radiometric profiles and prepare data for their satellite validation and algorithm

development activities.

With regards to the latter, recent work has

suggested that the uncertainty associated with

derived parameters, such as water-leaving

radiance, may be significantly reduced when a

single processor prepares the data (Hooker et al.

2001).

 In-water optical properties, such as

downwelling irradiance and upwelling radiance,

are analyzed using interactive software (Figure

4.4), internally known by the SPO as Visual

SeaBASS, written in the Interactive Data

Language (IDL) programming environment

developed by Research Systems, Inc. Visual

SeaBASS was developed to display and

evaluate profiles of optical properties and to

estimate near-surface values from these profiles

(Mueller 2002). Users are provided a variety of

options when defining the extrapolation interval

for the computation of near-surface values,

including the ability to remove outliers through

statistical filtering. Other features include a

capability to adjust radiance values to minimize

instrument self-shading effects (Zibordi and

Ferrari 1995) and the ability to load additional

oceanographic data (for example, water
The SeaWiFS Bio-Optical Archive and Storage System...

27

temperature profiles) for comparison with the

radiometric casts.

The main Visual SeaBASS window displays

both the radiometric depth profiles and the

estimated near-surface radiometric spectra. For

qualitative comparison, the spectral plots also

include theoretical surface values, calculated

using three well-validated bio-optical

algorithms. Currently, water-leaving radiance,

clear sky downwelling irradiance, and remotesensing reflectance spectra are estimated using

the models described in Gordon et al. (1988),

Frouin et al. (1989), and Morel and Maritorena

(2001), respectively. The theoretical in-water

spectra are used for qualitative comparison only,

as these algorithms were developed for Case 1

waters (Morel and Prieur 1977) and are not

always appropriate for direct comparison with

the near-shore or colored dissolved organic

matter (CDOM) dominated water studied by

many SeaBASS contributors. Such

comparisons of estimated values with

theoretical clear-water and clear sky maxima,

however, have proven valuable in distinguishing

erroneous or contaminated profiles.

Surface radiances estimated using Visual

SeaBASS are further evaluated by comparing

band ratios of the estimated values with those of

the theoretical values. Normally, all wavebands

shorter than 555 nm are normalized to 555 nm, a

wavelength thought to be one of the most

invariant for the widest range of water types.

The shapes of the estimated and theoretical

spectra are further compared by normalizing

each spectra to its integrated area (i.e., area

under the curve). Such integration eliminates

differences due to magnitude so that the spectral

shapes may be directly compared. Both

analyses assist in distinguishing erroneous or

contaminated wavebands, as they illustrate

variations or inconsistencies in the full spectra.

When long running time series of data are

available (for a particular locality, station, or

region of interest) the newly submitted data are

compared with these historical values (Figure

4.5), a practice which assists in evaluating the

radiometric stability of the field instruments.

Note that outliers located in the latter analyses

are not excluded from ingestion into the data

archive, as such evaluations are purely

qualitative and subjective. Rather, the data are

kept intact and the contributor is contacted in an

attempt to resolve any possible source(s) of

contamination and explain any differences.

Last, submitted radiometric and pigment data

are prepared for the SPOYs satellite-to-in situ

match-up analyses (Bailey et al. 2000). In the

event of multiple radiometric profiles per

station, the data are further evaluated to select

single representative spectra for each station

(Figure 4.6). A governing philosophy of the

match-up analyses is the need to compare the

satellite data product with a single ground truth

measurement per date and location. Normally,

this single spectrum is defined as that collected

under the clearest or most stable sky conditions

(determined using downwelling irradiance data

collected by a shipboard reference sensor) or as

the data with the clearest water-leaving radiance

value at 490 nm, another indication of favorable

atmospheric conditions. Replicate pigment

measurements are normally averaged.

Atmospheric data submitted to SeaBASS, in

particular, AOT, are subject to a similar series

of QC standards. These protocols and analyses

are documented elsewhere (Fargion et al. 2001,

Mueller et al. 2002a and 2002b) and will not be

discussed further in this report.

4.7 Data ingestion

Once the SeaBASS Administrator finishes

evaluating the incoming data set, the data files

are organized, cataloged and ingested into the

SeaBASS archival system (as described in

Chapter 5 of this report). Upon completion of

the latter, the data and data files are freely

available to authorized users via the World

Wide Web (as outlined in Chapter 6 of this

report).

The contributor is contacted if problems

occur or the data set cannot be archived for any

reason. Data prepared by the SPO for their

validation and merger activities are generally

not made available to the community, but may

be distributed to interested, appropriate parties

for additional analysis upon request.
The SeaWiFS Bio-Optical Archive and Storage System...

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Figure 4.5 A representative example of a time series analysis of radiometric data, specifically,

remote-sensing reflectance, collected on a long-term field campaign. Such analyses are used to

help verify the radiometric stability of data archived in SeaBASS.
The SeaWiFS Bio-Optical Archive and Storage System...

29

4.8 Updates

The SPO encourages all contributors to

update and correct their submitted data sets.

Records are maintained of updates and

corrections and the updated data are stored

offline. A summary of new and updated data

is posted online at:

<http://seabass.gsfc.nasa.gov/cgi-bin/seabass_news.cgi>.

The contributor maintains the responsibility

of ensuring that the current data in the archive

is identical to that used in the contributorIs

most recent publications or current research.

Figure 4.6 A representative example of how replicate surface spectra measured at a single station

are compared with the purpose of assigning a single representative spectrum to the station. Stations

are defined using narrow temporal and spatial boundaries.
The SeaWiFS Bio-Optical Archive and Storage System...

30

Chapter 5

SeaBASS Architecture and RDBMS Design

5.1 Introduction

In building SeaBASS, the SPO was tasked

with creating a system to archive, catalog, and

distribute bio-optical data and relevant

documentation. It required a repository with

holdings that were queriable and available via

the World Wide Web, secure enough to limit

access to authorized users, and accessible by all

computer platforms. Further, the design needed

to be easily expandable and flexible enough to

accommodate large data sets and multiple data

types. As discussed in Chapter 3 of this report,

to satisfy several of these prerequisite

conditions, SeaBASS data files adhere to the

basic ASCII format. The current chapter

outlines how such data files are ingested,

organized, and stored at NASA Goddard Space

Flight Center.

The current architecture of the SeaBASS

system consists of two principal components: a

directory tree structure, where the data files and

documentation are organized and stored, and a

RDBMS used to further catalog, archive, and

distribute the data. All submitted data files and

documentation reside permanently in the

directory tree. For each file, metadata from the

header arguments, its location in the directory

tree, and some geophysical data are stored in the

RDBMS. As such, the RDBMS may be queried

to compile information about the bio-optical

data set or to locate certain data. The tandem

use of these components provides a proficient

means for the SPO to archive and catalog their

data holdings. In conjunction with a series of

online CGI forms that interface with the

RDBMS (described in detail in Chapter 6 of this

report), these components also provide an

effective means for authorized users to search

the bio-optical holdings and obtain specific data.

5.2 Data ingestion

Once the evaluation of a submitted data set is

complete, the SeaBASS Administrator moves

the data files and documentation from the

SeaBASS FTP site to an appropriate location in

the directory tree. Data and metadata included

in the data files are then ingested into the

RDBMS using additional software, written in

PERL and Transact-SQL, an extension of the

Structured Query Language database

programming environment. The software

system gathers information from each data file

by parsing the header and data blocks. This

information is loaded into a series of linked

RDBMS tables using SQL stored procedures

and bulk copy commands. Upon completion,

the data are fully included in the bio-optical data

set and immediately available to authorized

users (as described in Chapter 6 of this report).

5.3 The data archive

All data files, related documents, and

instrument calibration files are stored in a

directory tree structure (Figure 5.1), residing on

a dedicated server at NASA Goddard Space

Flight Center. The directory tree is organized

by affiliation of the contributing PI, experiment,

and specific cruise. Each cruise directory has

additional subdirectories where the data files,

documentation, and other related files are

stored. Typically, the data files reside in a

subdirectory named Zarchive[, and supporting

documents, images, global and regional maps,

and calibration files in subdirectory named

Zdocuments[. A third subdirectory, named

Zraw[, is occasionally created by the SeaBASS

Administrator to store administrative comments,

SPO processing code, and previous versions of

updated data files.
The SeaWiFS Bio-Optical Archive and Storage System...

31

Individuals with full access to the bio-optical

archive may peruse the SeaBASS directory tree

by pointing their Web browsers to:

<http://seabass.gsfc.nasa.gov/SEABASS_ARCHIVE>.

As valid SeaBASS username and password is

required, this online index is not available to the

general public. Note, also, that the QarchiveR

and QdocumentsR subdirectories are available

for perusal by authorized users, however, the

QrawR subdirectory is not.

5.4 The relational database

management system

The SeaBASS RDBMS was built using the

SQL Server product from Sybase, Inc. Its

design consists of a series of tables (Figure 5.2,

Table 5.1), in the third normal form, used to

store both metadata from each header keyword

of a file and certain geophysical data values

from the file]s data block. To enhance query

performance, the server is configured for

parallel data access using multiple computer

processors. In addition, most database objects

reside on their own physical device and data are

frequently distributed across multiple partitions.

The SeaBASS Administrator regularly

addresses RDBMS performance and tuning

issues and implements new logic, as the

standard user base continues to expand. The

table architecture is such that users may query

the RDBMS for metadata or data from a single

file, or all data archived for a given institution,

contributor, experiment, data type, data

parameter, or spatial and temporal range. The

architecture may be easily expanded to

accommodate new data types or metadata

Figure 5.1 A representative example of the organization of the SeaBASS archive directory tree.

Data are organized by the affiliation of the contributing PI, experiment, and specific cruise.

The subdirectories QarchiveR and QdocumentR are used to store data files and supporting

documentation, respectively.
The SeaWiFS Bio-Optical Archive and Storage System...

32

elements and can comfortably manage large

data sets.

Additional metadata tables are occasionally

added to the system to accommodate new online

resources (refer to Chapter 6 of this report for

additional details) or SPO administrative

software. The administrative RDBMS tables

and software exceed the scope of this report and

will not be discussed further.

The RDBMS ingestion software first parses

the header block, evaluating each header

keyword and argument, and loads this

information into the appropriate table. Each

header keyword has an analogous column in one

or more RDBMS tables (Table 5.1). The system

is normalized such that separate tables exist for

contributor affiliations, contact information,

cruise particulars, and details relating to each

data file. The latter includes both ancillary data,

such as wind speed and wave height, and other

statistics about the data file, including the date

the data were archived and the data status, if, for

example, the data had been resubmitted. Once

the headers have been examined, the data block

is parsed. The date, time, latitude, longitude,

station name, and measurement depth of each

data record is stored in an additional RDBMS

table. Certain geophysical data values are

loaded into additional RDBMS tables. 

As of August 2002, all fluorometric and

HPLC pigment concentrations, sun photometer

data, including AOT, column water vapor, and

total column ozone, and discrete hyperspectral

spectrophotometer data are included in

additional, separate, RDBMS data tables. All

other data are available only as complete data

files (those residing in the SeaBASS archive

directory tree). The system, however, may be

easily expanded in the future to include

RDBMS tables for other geophysical data, such

as that from depth profiles and flow-through and

moored systems.
The SeaWiFS Bio-Optical Archive and Storage System...

33

Figure 5.2 The data model for the SeaBASS RDBMS. Each box represents a table, with the

table name listed on top (in capital letters) and column names provided inside the box. A

circled IPK and IFK designate primary and foreign keys, respectively. The box I(DATA

TABLE)K is a generic listing for several tables that hold geophysical data values.
The SeaWiFS Bio-Optical Archive and Storage System...

34

Table 5.1 The SeaBASS RDBMS tables with their associated header keywords and descriptions, as

of August 2002. The record I( DATA TABLE )N is a generic listing for several tables that hold

geophysical data values. Currently, data tables exist for phytoplankton pigment concentrations, sun

photometer data, and discrete hyperspectral spectrophotometer data.

Table name Related header

keywords Table contents and description

affililiations /affiliation The universities, laboratories, and organizations of all

contributors to SeaBASS.

contacts /contacts

/investigators

Contact information for each principal contributor of data to

the archive.

cruise_info /cruise

/experiment

A list of experiments and specific cruises with data in the

archive. References the principal contributor of data for

each record.

data_info

/east_longitude

/end_date

/end_time

/measurement_depth

/north_latitude

/south_latitude

/start_date

/start_time

/station

/west_longitude

The date, time, latitude, longitude, depth, and station of each

archived data measurement.

file_info

/calibration_files

/cloud_percent

/data_status

/data_type

/documents

/fields

/investigators

/secchi_depth

/water_depth

/wave_height

/wind_speed

One record for every file in the bio-optical data set.

References the cruise on which data in the file were

collected. Notes, using a status index, which data were

loaded into data tables, and indicates if the data were

submitted to the NODC. Includes general information about

each file, such as the date data were archived, the status of

the data (if, for example, the data are updates of previously

submitted data), and the type of data in the file. Also

includes a full list of contributors and data parameters, such

as CHL and AOT, and references the documentation and

instrument calibration files that accompany the data file.

Finally, provides additional oceanographic and atmospheric

data associated with the data in a given file.

hyperspectral /fields

An inventory of data parameters and the range and interval

of wavelengths for each hyperspectral radiometric

measurement.

multispectral /fields An inventory of data parameters and nominal wavelengths

for each multispectral radiometric measurement.

scan_range /fields

An inventory of data parameters and the range and interval

of wavelengths for each discrete hyperspectral scan,

including laboratory spectrophotometer and above water

radiometer scans.

unit_info /fields

/units

A list of standard data parameter names and their respective

units.

( DATA TABLE ) /fields Geophysical data values.
The SeaWiFS Bio-Optical Archive and Storage System...

35

Chapter 6

Database Access and Online Resources

6.1 Introduction

The purpose of this chapter is twofold: to

present methods of accessing the bio-optical

data set and to describe available online

resources. The SeaBASS World Wide Web

home page, located at

<http://seabass.gsfc.nasa.gov>,

provides a complete description of the systemGs

architecture, comprehensive documentation of

access policies and submission protocols, and

direct access to the bio-optical data set. Most of

the details documented in this report are also

posted on the Web site, where they may be

updated and amended as the need arises. Note

that, when appropriate, the addresses of

associated and relevant Web pages have been

provided in other chapters. Many of these

descriptive Web pages are self-describing and

will not be discussed further in this report.

The Web site also includes supplementary

resources, all of which are updated regularly,

such as tables of new and updated archived data,

answers to frequently asked questions, detailed

contact information, and interactive mapping

routines. In addition, results from the SPOsponsored satellite-to-in situ match-up analyses

(Bailey et al. 2000) and the SeaWiFS Biooptical Algorithm Mini-workshop (SeaBAM)

(OGReilly et al. 1998) are available via the

SeaBASS home page. The methods and results

from the latter activities are described in the

references provided and will also not be further

addressed.

Every resource listed above is freely

available for public use, with the exception of

access to the restricted data set, currently

defined as all data collected after 31 December

1999. Web pages providing access to restricted

data require a username and password. The

SeaBASS Data Access Policy and the process of

applying for a username and password are both

described in detail in Chapter 2 of this report.

6.2 Bio-optical data set access

Data and files from the bio-optical data set

may be accessed and saved using a series of

online search engines (Table 6.1) provided at:

<http://seabass.gsfc.nasa.gov/dataordering.html>.

Each search engine is a CGI form (Figure 6.1)

that interfaces with the SeaBASS RDBMS.

Using the form, visitors may limit queries to

particular experiments, contributors, date and

location ranges, and data types (for a description

of SeaBASS data types, refer to Chapter 3 of

this report). Linked to each search engine are a

series of supplementary Web pages with tables

listing additional relevant information, for

example, the names of archived experiments or

data types, to assist users narrow or tailor their

queries. On occasion, Java pop up windows are

used to provide definitions or explanations of an

online feature.

When a user submits a query, the software

polls the RDBMS and generates a list of

corresponding data files or values which meet

the search criteria. Items in the returned list

may subsequently be viewed using the clientGs

Web browser, saved locally, and in some cases,

mapped or plotted using additional online

software. In several instances, two versions of a

given CGI form exist, one of which is

password-protected and another which

accessible by the general public. Both versions

are identical, with the exception that only data

collected prior to 31 December 1999 are

available to the public.

Upon the completion of a query, an

electronic mail message is sent to the SeaBASS

Administrator. The message notifies the
The SeaWiFS Bio-Optical Archive and Storage System...

36

Figure 6.1 A representative example of an online CGI form used to query the SeaBASS bio-optical

data archive.

Administrator that a online query of the

RDBMS has been executed and describes the

particular search parameters. The Web server

and the search engine software also log all user

activity. This information is made available to

all data contributors upon request.

When a visitor selects data files to be saved,

these files are compiled into a single tar (UNIX

tape archive) bundle which is created on the

SeaBASS FTP site at:

<ftp://samoa.gsfc.nasa.gov/seabass/outgoing>.

Likewise, all geophysical data to be saved are

written to a single file placed on this FTP site.

Both may be downloaded locally using standard

FTP or via the clientWs Web browser. Users

operating on Microsoft Windows and Macintosh

platforms may need to install additional thirdparty software to extract the individual data files

from the tar bundle.

6.2.1 Data search engines

Several search engines are available to locate

and extract data files and geophysical data

values from the bio-optical data set. The most

comprehensive search engine, the SeaBASS

Bio-optical Search Engine, available at:
The SeaWiFS Bio-Optical Archive and Storage System...

37

Table 6.1. Online resources for extracting and manipulating data from the SeaBASS bio-optical

data set. BRestrictedD indicates the data are part of the restricted data set and a username and

password is required for access. BPublicD indicates the data are available to the general public. As

of August 2002, all data collected prior to 31 December 1999 are publicly available. Each resource

is available via the SeaBASS Web site at <http://seabass.gsfc.nasa.gov/dataordering.html>.

Utility Access Description

Bio-optical Search Engine Restricted, Public

The principal utility for searching the full bio-optical data

set. Queries return a list of files, which are available to view

and save. Additional online resources may be used to plot

and map the data in a returned file(s).

Pigment Locator Restricted, Public

The search engine used to access directly the fluorometric

and HPLC phytoplankton pigment data included in the biooptical data set. Queries return a list of geophysical data

values, which are available for download.

Aerosol Locator Restricted, Public

The search engine used to access directly the AOT and other

sun photometer data included in the bio-optical data set.

Queries return a list of geophysical data values, which are

available for download.

General Search Engine Public

The principal utility used to compile, from the bio-optical

data set, generic information about a cruise, contributor, data

type, or date or location range. Queries return a table of

archived cruises and a list of data contributors and

parameters associated with each. Additional online

resources may be used to map data from a specific cruise.

Cruise Search Engine Public

A search engine used to compile generic information about

cruises included in the bio-optical data set. Queries return

date and location ranges, data contributors, and the data

types and parameters collected.

Validation Cruise Search Engine Public

The search engine used to locate potential validation data

sets for a specific, user-defined satellite mission. Queries

return a list of cruises and their date range, center latitude

and longitude, data contributors, and data parameters.

Archive Directory Tree Restricted

The directory structure used to organize and store the data

files included in the bio-optical data set. The data files,

supporting documentation, and instrument calibration files

are all available for perusal.

Mapping Utility Public

A utility for generating maps of SeaBASS data points based

on customized date, location, and parameter inputs.

Additional resources include a global map of all data

included in the bio-optical data set and mission-specific

maps for OCTS/POLDER, SeaWiFS, MODIS Terra and

Aqua, and MERIS. All are updated daily.

<http://seabass.gsfc.nasa.gov/cgi-bin/seabass_search.cgi>,

provides full access to the bio-optical data set.

Queries return a list of matching data files,

which are available to view or download. In

addition, users may generate online maps and

plots of data from one or more files or download

relevant documentation. For this search engine,

users may not only limit queries to particular

date ranges, but also to defined monthly

climatologies (i.e., specific months for any
The SeaWiFS Bio-Optical Archive and Storage System...

38

given number of years). This utility provides

access to all data in the bio-optical data set.

Currently, two search engines are available

for extracting geophysical values from the biooptical data set, the SeaBASS Pigment Locator,

found at

 <http://seabass.gsfc.nasa.gov/cgi-bin/pigment_search.cgi>,

and the SeaBASS Aerosols Locator, located at:

<http://seabass.gsfc.nasa.gov/cgi-bin/aerosol_search.cgi>.

These utilities provide direct access to

phytoplankton pigment concentrations and sun

photometer data, respectively, included in the

bio-optical data set. Queries return a table of

geophysical data values, including ancillary

information, such as date, time, location, cruise

name, and contributor, which are available to

download. For both of these utilities, users

define the data parameters for which theyOd like

to search by navigating through a series of

checkboxes.

Finally, visitors with full SeaBASS accounts

may access the data archive directly via their

Web browser. Such users may peruse the

SeaBASS directory tree by visiting

<http://seabass.gsfc.nasa.gov/SEABASS_ARCHIVE>.

Here, all data files, supporting documentation,

and instrument calibration files comprising the

bio-optical data set are available to view or

download.

6.2.2 Metadata search engines

Other search engines are available for

compiling metadata relating to the bio-optical

data set. These provide generic information

about the data, such as cruise and experiment

names, date and location ranges, data

parameters collected, and contributor names.

They do not, however, provide access to

geophysical data values, and are therefore

available to the general public.

The utility of the metadata search engines is

twofold: visitors may compile general

information about data archived in SeaBASS

without directly accessing the geophysical data,

and queries return a summary or overview of

archived cruises, for example, date and location

ranges, whereas the data search engines do not.

The former is thought to be particularly useful

for (1) visitors without full access to the biooptical data set, who are interested in what has

been archived, (2) SeaBASS data contributors

desiring a simple, yet comprehensive, list of

their archived data, and (3) other researchers

searching for potential validation cruises for

their satellite validation activities.

Currently, the most versatile metadata search

utility is the SeaBASS General Search Engine,

available at:

<http://seabass.gsfc.nasa.gov/cgi-bin./general_info.cgi>.

Like the data search engines, queries may be

limited by particular experiments, contributors,

date and location ranges, and data types.

Queries generate a table of archived cruises and

the data types and parameters collected on each.

Subsequent Web pages, hyperlinked to each

cruise in the table, display more detailed

information about the given cruise, for example,

date and location ranges, and provide the user

the option of generating a regional map of data

points.

The SeaBASS Cruise Search Engine, located

at:

<http://seabass.gsfc.nasa.gov/cgi-bin/cruise_search.cgi>,

is a significantly simplified version of the

General Search Engine. Its design was arranged

to be more efficient for visitors interested in

particular archived cruises. Here, visitors enter

only a cruise name, or a search string. Queries

return the date and location range, data

contributor(s), and data types and parameters for

each matching cruise. In addition, users are

provided the option of generating a regional

map of data points for each cruise.

The last metadata search engine, the

SeaBASS Validation Cruise Search Engine,

available at:
The SeaWiFS Bio-Optical Archive and Storage System...

39

<http://seabass.gsfc.nasa.gov/cgibin/validation_cruises.cgi>,

operates somewhat differently than the others.

This utility was designed specifically to assist

researchers requiring potential validation cruises

for their satellite calibration and validation

activities. As such, queries may be limited only

by satellite mission. Current options include the

Ocean Color and Temperature Scanner (OCTS)

/ POLDER, SeaWiFS, MODIS Terra and Aqua,

and MERIS. Queries return a table of potential

validation cruises. Each record in the table

includes the data contributor(s), the data type

collected, the start and end dates, and the center

latitude and longitude coordinates for the given

cruise. As with the others, users are provided

the option of generating a regional map of data

points for each cruise.

6.3 Other online utilities

6.3.1 Maps

Visitors wishing to generate maps of

SeaBASS data may do so interactively using the

SeaBASS Mapping Utility, available at:

<http://seabass.gsfc.nasa.gov/cgi-bin/seabass_map.cgi>.

The default map is global, however, users are

provided the option of customizing latitude and

longitude boundaries. Mapped data points may

be further limited by user-defined date ranges

and specific data parameters (e.g., WchlX and

WAOTX). In the event more than one data

parameter is specified, users may restrict

mapped points to those where all parameters

were collected; otherwise, all data where any

matching parameter was collected will be

included in the map.

Several other global maps are linked to this

Web site: (1) a map of all data included in the

bio-optical data set, and (2) mission-specific

maps of pigment, radiometer, and sun

photometer data points. Currently, the latter

includes maps for OCTS / POLDER, SeaWiFS,

MODIS Terra and Aqua, and MERIS. All of

the above are updated daily and are available for

download.

6.3.2 News and updates

All changes made to SeaBASS, including

both system updates and the archival of new and

updated data, are documented online at the

SeaBASS New and Updates page, located at:

<http://seabass.gsfc.nasa.gov/cgi-bin/seabass_news.cgi>.

The first half of this site is reserved for news of

recent additions and modifications to the

SeaBASS RDBMS and Web site. A brief

summary of each update, the date of each

update, and hyperlinks to relevant Web sites,

when available, are all posted.

The remainder of the site is dedicated to

posting information about recently submitted

bio-optical data sets. The principle component

is a table that lists details about data submitted

within the past three months. The table includes

the data contributor, the date data were

submitted, the data status (either new or update),

the experiment and cruise names(s), and the data

parameters provided. Each record also includes

two hyperlinks: one to the data_s position in the

archive directory tree, which is accessible only

to visitors with full access to the bio-optical data

set; and another to an additional Web page that

lists more detailed information about the

cruise(s), for example, date and location ranges,

and provides a regional map of data points.

With the exception of the link to the archive

directory tree, the information on this Web page

is available to the general public.

Also provided on this site is a link to the

SeaBASS Email Notification Service, located

at:

<http://seabass.gsfc.nasa.gov/cgi-bin/seabass_mail.cgi>.

Interested parties may join the SeaBASS

Updates mailing list by completing and

submitting the electronic form provided at this

site. An electronic message listing recently

submitted data is sent to members of this list
The SeaWiFS Bio-Optical Archive and Storage System...

40

once a week. Only cruises archived in the past

week are included in the electronic message.

6.3.3 Historical data sets

The SPO maintains two additional Web sites

relating to other global bio-optical data sets,

both of which are available via the SeaBASS

Web site. The first, the SeaWiFS calibration

and validation historical pigment database

(Firestone and McClain 1994), was originally

assembled to assist in evaluating satellite

pigments retrivals. It is located at:

<http://seabass.gsfc.nasa.gov/cgi-bin/pigment_query.cgi>,

and includes only measurements of chlorophyll

a and phaeophytin pigment concentrations.

The second, the SeaWiFS Bio-optical Miniworkshop (SeaBAM) data set (ORReilly et al.

1998), was assembled to develop and evaluate

the operational SeaWiFS chlorophyll a and

CZCS-like pigment algorithms. It is located at:

<http://seabass.gsfc.nasa.gov/seabam/seabam.html>.

and includes coincident radiometric

observations and chlorophyll a concentrations.

The SeaBAM Web site also includes details

about the candidate algorithms and results from

the workshop. The two data sets are described

in detail in the provided references and will not

be discussed further in this report. Note,

however, that most data from both sets has

subsequently been archived in the SeaBASS

bio-optical data set.

6.3.4 NODC

In December 2001, the public data from the

bio-optical data set, those collected prior to 31

December 1999, were released to the NODC for

inclusion in their national archive. This

submission is available via their Web site at:

<http://www.nodc.noaa.gov/col/projects/access/ seabass.html>.

Additional details regarding the access and

acknowledgement policies for these data are

provided in Chapter 2 of this report.

6.4 User statistics

As of August 2002, 35 research groups

outside of the SPO have been granted full access

to SeaBASS. From 1 January 2002 through 31

July 2002, these groups queried SeaBASS over

800 times and downloaded more than 42,000

data files from the bio-optical data set. During

the same time period, 97 research groups

searched the public data set 375 times and

downloaded over 22,000 files.
The SeaWiFS Bio-Optical Archive and Storage System...

41

Glossary

AERONET Aerosol Robotic Network

AOT Aerosol Optical Thickness

ASCII American Standard Code for Information Interchange

CDOM Colored Dissolved Organic Matter

CGI Common Gateway Interface

CZCS Coastal Zone Color Scanner

FTP File Transfer Protocol

GLI Global Imager

HPLC High Performance Liquid Chromotography

IDL Interactive Data Language

IP Internet Protocol

LINUX A UNIX-type operating system developed under the GNU General Public License

MERIS Medium Resolution Imaging Spectrometer

MODIS Moderate Resolution Imaging Spectroradiometer

NRA NASA Research Announcement

NASA National Aeronautics and Space Administration

NOAA National Oceanic and Atmospheric Administration

NODC National Oceanographic Data Center

OCTS Ocean Color and Temperature Scanner

PERL Practical Extraction and Report Language

POLDER Polarization and Directionality of the Earth's Reflectances

QC Quality Control

RDBMS Relational Database Management System

SCOR Scientific Committee on Oceanic Research

SeaBAM SeaWiFS Bio-optical Mini-workshop

SeaBASS SeaWiFS Bio-optical Archive and Storage System

SeaWiFS Sea-viewing Wide Field-of-view Sensor

SI International System of Units

SIMBIOS Sensor Intercomparison & Merger for Biological & Oceanic Interdisciplinary Studies

SPO SeaWiFS / SIMBIOS Project Office

SQL Structured Query Language

UNIX Uniplexed Information and Computing System
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42

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