=Paper=
{{Paper
|id=Vol-1328/GSR2_Rasaiah
|storemode=property
|title=A Novel Metadata Standard for In Situ Marine Spectroscopy Campaigns
|pdfUrl=https://ceur-ws.org/Vol-1328/GSR2_Rasaiah.pdf
|volume=Vol-1328
|dblpUrl=https://dblp.org/rec/conf/gsr/RasaiahJB12
}}
==A Novel Metadata Standard for In Situ Marine Spectroscopy Campaigns==
https://ceur-ws.org/Vol-1328/GSR2_Rasaiah.pdf
A novel metadata standard for in situ marine spectroscopy campaigns
Barbara Rasaiah, Simon Jones, Chris Bellman
RMIT University
Melbourne, Australia
barbara.rasaiah@rmit.edu.au, simon.jones@rmit.edu.au, chris.bellman@rmit.edu.au
Tim Malthus
CSIRO Land and Water
Canberra, Australia
tim.malthus@csiro.au
ABSTRACT
Metadata are an important component in the cataloguing and analysis of in situ spectroscopy datasets because of their
central role in identifying and quantifying the quality and reliability of spectral data and the products derived from them. This
paper presents approaches to constructing a novel metadata standard for marine spectroscopy that serves to ensure a high level of
reliability, integrity, and longevity for a spectroscopy dataset. Examined are the challenges presented by designing a standard that
meets the unique requirements of in situ marine spectroscopy datasets, including the special case of measuring reflectance for
underwater coral targets. Issues such as field measurement methods, instrument calibration, and data representativeness are
investigated. The proposed metadata model incorporates expert panel recommendations that include metadata protocols critical to
all campaigns, and those that are restricted to campaigns for specific marine environments. The implication of semantics and
syntax for a robust and flexible metadata standard are also considered. Approaches towards an operational and logistically viable
implementation of a schema are discussed. This paper also proposes a way forward for adapting and enhancing current geospatial
metadata standards to the unique requirements of field spectroscopy.
Keywords: Remote Sensing, Databases, in situ Observations, Metadata, Field Spectroscopy
1 INTRODUCTION
Data collection protocols, encompassing both field spectral measurement methods and the metadata associated with them vary
widely across the breadth of scientific inquiry applied to in situ spectroscopy. Metadata is a central component to the reliability,
integrity, and legacy of a spectroscopy dataset because it serves to mitigate systematic and random errors on recorded radiance,
target discriminability and contrast (Duggin, 1985) and reduce system bias and variability (Pfitzner et al., 2006). On international
and national scales, ad hoc data collection protocols are the norm as no formal standards exist within the remote sensing
community for in situ metadata collection and rather arise from the expertise and knowledge of the scientists carrying out the
campaign. Metadata recorded during a campaign may vary in format (hardcopy log sheets, excel forms, rudimentary database) and
in volume (inclusive of documentation of all relevant campaign protocols to a minimum of metadata describing only the target
being sampled). Metadata collection protocols diverge along the lines of the purpose of the campaign (calibration and validation,
creation of a spectral library) and the target (tree crown, soil, seagrass, etc). Logistics, environment, instruments and target type all
affect the design and implementation of a practical metadata standard.
Here the special case of a metadata standard for a marine campaign for underwater coral reflectance is presented. Marine
campaigns are unique from terrestrial campaigns in terms of the instrumentation, specialized requirements for in situ data
collection and environmental variables. Targets can include seagrass, macro-algae, corals and sponges, spectral measurements
may be taken above surface or below surface and opinions differ on how inclusive a metadataset must be to document
environmental and target properties (Bhatti et al., 2009 and Dekker et al., 2010). Instrument housing is often necessary to permit
submersion and in some instances the instrument must be specially adapted to the underwater light field. Spectral measurements
are recorded in a potentially unsafe environment with often continuously variable viewing conditions (illumination, viewing
geometry, turbidity, etc.). At the University of Queensland, a customized underwater spectrometer system was developed and
tailored specifically to coral reef ecology, and the ecology and physiology of animal colour vision. The accompanying protocols
for recording metadata in situ are interdependent with the challenges of radiometric data collection underwater as they are
designed to simultaneously ensure the requisite operator safety (Roelfsema et al., 2006).
2 A SPECIALIZED MARINE SPECTROSCOPY METADATA STANDARD
To ensure a high quality and practical metadataset, a metadata standard for underwater coral reflectance should have the following
properties: 1) the metadata fields are sufficient to comprehensively and explicitly document the activities that took place and
quantify and qualify influencing factors to the spectral measurement 2) allow replication of the campaign if required 3) and be
flexible and broad enough in the scope of data capture to permit interoperability with other datasets. Granularity (the degree of
specificity of the variable being recorded), syntax of the fields, and their data format (numeric/text/timestamp) affects the potential
for data export, mining, and sharing.
Presented here (Table 2.1) is a metadata standard for underwater coral reflectance spectroscopy. It is derived from input from an
expert panel of marine remote sensing scientists at the ACEAS (Australian Centre for Ecological Analysis and Synthesis) Bio-
optical workshop held in Australia in 2012. While not inclusive of all metadata (instrument, calibration activities, reference
standards, etc.) that should be recorded for an in situ campaign, it documents those metadata that describe field methods and
variables unique to underwater coral reflectance measurements. The metatadaset is divided into four main categories: ‘Location
and Environment Information’, ‘Illumination Information’, Viewing Geometry’, ‘Coral Target Properties’. A description and
reasons for inclusion of each field is provided, as well an example of each. An optionality designation of either ‘Critical’ or
‘Useful’ has been assigned to each field. Assuming that campaign logistics are not always favourable to documenting all
necessary metadata, a prioritization model for criticality can form the basis of a standard that is both practical and fits the purpose
for which the data is being collected. Critical fields are those that ensure the integrity of the dataset and cannot be excluded; useful
fields are those that increase the robustness of the dataset for purposes beyond which it was originally intended. The data type
specifies the most suitable format (text/numeric/timestamp/binary/image) for a given metadata parameter. A ‘GML Object Type’
column is included to indicate those metaparameters that can be expressed as GML 3.3 (Geographic Markup Language) objects.
GML 3.3 is an implementation of ISO 19107 (specifying conceptual schemas for geographic features) and is used
here simply as an example of a vocabulary that could be used to implement the metaparameters as objects in
a metadata schema. Reference to a standard vocabulary, such as that provided by GML, permits translating the standard into
a schema with maximum interoperability.
The most populous category (23 fields) is ‘Location and Environment Information’. This is due to the high number of variables
found within the marine environment that influence spectral measurements (water column properties, subsurface conditions,
CDOM, etc.). There are commonalities with terrestrial campaigns (GPS coordinates, location description) but even in these cases
special considerations must be made for the feasibility of recording these in situ. The ‘Illumination Information’ metadata
category, while again sharing common fields with other non-marine campaigns, must make allowances for wave lensing and
artificial light fields. The ‘Viewing Geometry’ category is identical to metadata requirements for most terrestrial campaigns
except for documenting an operator’s position relative to the target when they must provide shading over the target with their
body to compensate for the fluctuating light field. The ‘Coral Target Properties’ category, similar to ‘Location and Environment
Information’, contains fields relevant to marine campaigns only and reflects the special requirements of documenting underwater
coral reflectance measurements.
Table 2.1 Metadata standard subset for underwater coral reflectance measurements
Location Information Metadata
REASON FOR
OPTIONALIT DATA
METADATA FIELD INCLUSION / EXAMPLE GML OBJECT TYPE
Y TYPE
COMMENTS
Qualitative
description of
Location description Useful 5 km offshore text gml:location
surrounding
environment
Permits referencing
to
Critical gml:CoordType
aerial/satellite/other
campaigns
GPS coordinates x,y,z
Difficult to do; done
numeric
on the dive site
Coordinates, datum +
projection can be
determined from
Google Earth
Substitutes GPS
Manual coordinate coordinates in
Useful gml:CoordType
determination with map instances of poor x,y numeric
and compass positional accuracy
Provides additional
visual data where
Reference to photo of recording additional
photo # or
local relevant metadata of target Critical text gml:stringOrNull
name
environment + target and environment is
not possible or
feasible
Date of associated Provides timestamp
Critical 11/28/2012 timestamp gml:TimePositionUnion
photo for photo
Water type (freshwater, for water column Fresh/brackis
Useful text gml:CodeType
saltwater) profiles h/salt
From lowest
Depth gml:doubleOrNull
astronomical tide
Critical 18 m numeric
Above surface AOT/ atmospheric
gml:stringOrNull
conditions visibility/ clouds
Useful high ceiling text
qualitative
Subsurface conditions description of gml:stringOrNull
Useful 2m vis text
visibility
Input for determining
Wave height and
true depth relative to
period (for reflectance Critical 0.25 m numeric gml:doubleOrNull
datum and wave
measures)
lensing effects
Table 2.1 (continued) Metadata standard subset for underwater coral reflectance measurements
Location Information Metadata
Input for determining
Wave height and
true depth relative to
period (for radiance Useful 0.25 m numeric gml:doubleOrNull
datum and wave
measures)
lensing effects
Input for determining
Tide conditions true depth relative to
Critical 6:36 PM time gml:TimePositionUnion
H or L datum and wave
lensing effects
Swell, wave height, Input for determining Useful 1m numeric
gml:doubleOrNull
long period waves water column depth
optionality ranking
Wind speed dependent on severity Critical/Useful 5 kn numeric gml:Quantity
of conditions
optionality ranking
Wind direction dependent on severity Critical/Useful Ssw text gml:Direction
of conditions
Height of sensor from
surface (if for water column
Critical 1.75 m numeric gml:doubleOrNull
characterizing water profiles
column properties)
Depth of sensor from
for water column
surface (if profiling Critical 7m numeric gml:doubleOrNull
profiles
water column)
Reference to photo
Natural canopy illustrating canopy photo
Useful text gml:stringOrNull
structure structure surrounding filename
target
Suspended sediment
Not useful for habitat
concentration (for Critical #mgl -1 numeric gml:Quantity
spectral library
water column studies)
Chlorophyll for water column
Useful #mgl -1 numeric gml:Quantity
concentration profiles
Secchi disk
for water column
transparency/turbidity Useful M (?) numeric gml:Quantity
profiles
measure
Coloured dissolved
organic matter
CDOM spectral slope -S value numeric
for water column
Critical gml:Quantity
profiles
Coloured dissolved
organic matter
CDOM concentration A 440 nm numeric
for water column
Critical gml:Quantity
profiles
for water column 1200 µg C•l -
Detritus concentration Critical 1 numeric gml:Quantity
profiles
Phytoplankton for water column Gymnodiniu
Critical text gml:stringOrNull
species/classes profiles m spp.
Table 2.1 (continued) Metadata standard subset for underwater coral reflectance measurements
Illumination Information Metadata
REASON FOR
OPTIONALIT DATA
METADATA FIELD INCLUSION / EXAMPLE GML OBJECT TYPE
Y TYPE
COMMENTS
Description of
Optical measure of general illumination
diffuse light
ambient conditions conditions; useful Useful text gml:stringOrNull
field
(direct, diffuse) for water column
profiles
Source of illumination Type of halogen
Critical text gml:CodeType
(e.g. sun, lamp) illumination lamp
Input parameter for
Bulb intensity downwelling Useful 100 W numeric gml:Quantity
radiance calculation
Range of irradiance
Light spectrum Useful VIS/NIR text gml:stringOrNull
spectrum
Input parameter for
Single beam/multi beam downwelling Useful single boolean gml:boolean
radiance calculation
Target surface area
Beam coverage (as a exposed to bulb
Useful 25˚ numeric gml:degrees
degree measure) radiance varies with
beam spread
Used for cross-
Time interval for referencing weather
weather station data station data with Useful 15 min numeric gml:Quantity
logging time of spectral
measurement
Qualitative
Optical thickness of good
description of Useful text gml:stringOrNull
atmosphere visibility
visibility
Estimated
Visibility estimate quantitative Useful 100 km numeric gml:Quantity
visibility
Estimated
Cloud cover % percentage of sky Useful 25% numeric gml:Quantity
covered by clouds
octave /
Model used to
Cloud cover model Useful quadrant / text gml:CodeType
describe cloud cover
other
Cloud cover threshold Only useful if
Useful 50% text gml:Quantity
for this project overcast
Photo of sky (zenith to Qualitative visibility
Useful image
horizon) data
Can’t be measured
gml:boolean
in situ;
Wave lensing Useful yes/no boolean
Will know this from
wave height data
Only in seagrass, seagrass
Natural canopy shading Useful text gml:stringOrNull
branching corals shadowing
Shadowing with
diver’s body to
eliminate influences shadowing
Artificial light canopy
(eg. Wave lensing) Useful of target text gml:stringOrNull
effect
If measurement is from diver
from a boat, then
boat may shade
Table 2.1 (continued) Metadata standard subset for underwater coral reflectance measurements
Viewing Geometry Metadata
REASON FOR
DATA
METADATA FIELD INCLUSION / OPTIONALITY EXAMPLE GML OBJECT TYPE
TYPE
COMMENTS
Measure of
Distance from target distance of sensor Critical 0.75m numeric gml:doubleOrNull
from the target
Yes, if 3D
Distance from structure
Critical 3m numeric gml:doubleOrNull
bottom/substrate (seagrass,
branching coral)
Area of target in field of Calculated if FOV
Useful 100% numeric gml:Quantity
view specified
Declination of
Illumination zenith illumination
Useful 15˚ numeric gml:degrees
angle source from the
zenith
Horizontal angle
of illumination
Illumination azimuth
source measured Useful 205˚ numeric gml:degrees
angle
clockwise from a
north base line
Declination of
Sensor zenith angle sensor from the Useful 5˚ numeric gml:degrees
zenith
Horizontal angle
of sensor
Sensor azimuth angle measured Useful 75˚ numeric gml:degrees
clockwise from a
north base line
Degree measure of
adjusted field-of-
Foreoptic view of bareoptic Critical 8˚ numeric gml:degrees
fibre (due to
attached foreoptic)
Only applies if
Distance of operator there is presence
Critical 0.25 m numeric gml:doubleOrNull
from sensor of shading from
operator's body
Coral Target Properties Metadata
REASON FOR
DATA
METADATA FIELD INCLUSION / OPTIONALITY EXAMPLE GML OBJECT TYPE
TYPE
COMMENTS
Code identifier/tag
Target ID Critical Name code text gml:stringOrNull
for sample
Qualitative
Coral algae
Type descriptor of target Critical text gml:CodeType
etc.
type
Diploria
Species or name Coral species Critical text gml:stringOrNull
strigosa
Table 2.1 (continued) Metadata standard subset for underwater coral reflectance measurements
Coral Target Properties Metadata (continued)
Size (diameter) Size of target Useful 30 cm numeric gml:Quantity
Critical to
quantifying
Location description (in Lab/boat/in
environmental Critical text gml:CodeType
situ/on boat/in lab) situ
factors to spectral
measurement
Quantitative
Density of growth measure of density Critical 2.94 g cm-3 text gml:Quantity
of target
Qualitative
description of
Homogeneity/heterogen degree of homogeneou
Useful text gml:stringOrNull
eity homogeneity of s
target being
sampled
Attached photo
Homogeneity/heterogen
can be used as a Useful image
eity (photo)
reference
Useful for
endmember
Numerous
Presence of epiphytes analysis of Useful text gml:stringOrNull
epiphytes
spectral
measurements
Attached photo
Presence of
can be used as a Useful image
epiphytes(photo)
reference
Useful for
endmember
Benthic microalgae Chla
analysis of Useful text gml:stringOrNull
(absence/presence) sampling
spectral
measurements
Input parameter
for determining
upwelling
radiance/
Distance from bottom Critical 20 m numeric gml:doubleOrNull
background
reflectance
affecting spectral
measurements
Input parameter
for determining
upwelling
radiance/
Substratum height Critical 4m numeric gml:Quantity
background
reflectance
affecting spectral
measurements
Input parameter
for determining
upwelling
radiance/
Slope Useful 5% numeric gml:Quantity
background
reflectance
affecting spectral
measurements
Input parameter
for determining
upwelling
radiance/
Strike Useful 25˚ numeric gml:degrees
background
reflectance
affecting spectral
measurements
3 IMPLICATIONS FOR METADATA SHARING AND INTEROPERABILITY
A viable and practical metadata standard for underwater coral reflectance measurements must provide flexibility for data sharing
in a common exchange format, while being suitably comprehensive in documenting the data relevant to the campaign. In the
context of international data sharing of substratum and benthic spectral data, the establishment of standards for the capture,
storage, and use of spectral signature files with associated metadata is required due to the effect of environmental factors in
shallow water environments on the derived data (Dekker et al., 2010). The standard proposed in Section 2 can be easily
implemented as a schema in a common exchange format such as GML and XML (Extensible Markup Language). XML is self-
descriptive with extensibility features (Mahboubi and Darmont, 2010) and can facilitate progress towards integration of in situ
coral reflectance data with multi-dimensional remote sensing data sets, both within the marine context and near-shore terrestrial
campaigns. One of its greatest strengths is platform independence, and a framework for XML-based data interchange is espoused
in the Common Warehouse Metamodel, which includes XML Metadata Interchange (XMI) standards for datawarehouses
(Mangisengi et al., 2001 and Torlone, 2009). XML also facilitates searching and selection, it is human and machine readable,
platform independent, convertible to other formats and allows quick assessment of suitability for other research products (Malthus
and Shironola, 2009); it provides the greatest potential for data discoverability compared to the spectral archiving structures
currently used by marine scientists in coral spectroscopy campaigns (including excel sheets and text files). The XML format can
be easily accommodated in a variety of data archiving schema and software, including spectral libraries, databases, and
datawarehouses.
Large-scale implementation of standards for encoding and sharing coral reflectance metadata is best facilitated by national and
international agencies responsible for safeguarding and distributing these datasets. OGC (Open Geospatial Consortium) launched
the Marine Metadata Interoperability Project to make data available from various ocean observing systems (OGC, 2012); however
there are no specific metadata standards for in situ marine spectroscopy. IMOS (Integrated Marine Observing System, Australia)
provides NetCDF specifications for in situ marine observations but are biased towards biochemical sensors and recording
environmental variables, with no reference to spectroscopy measurements (IMOS, 2012). The ISO19115 sets of standards for
geospatial metadata provide general guidelines, but do not explicitly address the metadata requirements of marine field
spectroscopy collection techniques, or the ontologies and data dependences required to model the complex interrelationships
among the observed phenomena as data and metadata entities (ISO, 2012). The lack of international standards impedes wide-scale
mining and sharing of in situ marine spectroscopy datasets generated by remote scientists around the world. Adopting an XML-
based metadata model for coral reflectance measurements is an initial step in establishing the foundations for a standard.
4 CONCLUSION
A practical and viable metadata standard for in situ coral reflectance can be used to inform a common data exchange standard for
spectroscopy datasets in general. The model presented in this paper meets the requirements for a metadataset that is
comprehensive, explicit, allows replication of the campaign if required, and is suitably broad in the scope of data capture to permit
interoperability with other datasets. The standard is flexible by specifying both critical and useful metadata fields that are
populated dependent upon the logistics of the campaign and the purposes for which the data will be used. In situ spectroscopy
metadatasets are currently generated based on ad hoc data collection protocols that impede wide-scale data mining, sharing,
intercomparison and interoperability of datasets. A metadata model based on the standard proposed here, in a common exchange
format such as XML would facilitate convenient and practical data exchange among the remote sensing community.
ACKNOWLEDGEMENTS
Marine remote sensing scientists at the ACEAS (Australian Centre for Ecological Analysis and Synthesis) Bio-optical workshop
held in Australia in 2012 who generously provided input to the coral reflectance metadata schema proposed here.
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Author Biographies
Barbara Rasaiah is a PhD candidate at RMIT University in Melbourne, Australia, investigating approaches to
a coordinated evolution of hyperspectral metadata protocols, field spectroscopy methods and data exchange
standards within the hyperspectral remote sensing community. Barbara’s work has been presented at the
ISRSE 34 conference, 7th EARSeL workshop, and ISPRS 2012. Barbara has an educational background in
computer science and mathematics and has worked in industry as a computer programmer, web designer, and
computer operations analyst. She was awarded the 2012 Goetz Instrument Award from ASD Inc., for novel
and innovative research in field spectroscopy.
Simon Jones is professor of remote sensing and director of the Remote Sensing and Photogrammetry Research
Centre at RMIT University in Melbourne, Australia. His current projects include leading research at TERN
(Terrestrial Ecosystem Research Network), Commonwealth Environment Research Fund Hub “Landscape
Logic”, and organising the 2012 ISPRS International Congress on Photogrammetry and Remote Sensing.
Simon’s specializes in remote sensing, ground verification (in situ observations), spatial analysis, spatial data
uncertainty, land-cover mapping, monitoring & modelling and vegetation. He is a foundation member and
former director of the (Surveying and) Spatial Sciences Institute, Australia and has previously worked at the
Joint Research Centre of the European Commission (Global vegetation Monitoring Unit).
Chris Bellman is associate professor and discipline head of geospatial science at RMIT University in
Melbourne, Australia. His current projects include organising the 2012 ISPRS International Congress on
Photogrammetry and Remote Sensing. Chris specializes in photogrammetry, GIS and spatial analysis and
computer-aided mapping. He is a previous president of the Surveying and Spatial Sciences Institute of
Australia. Chris is winner of the 2008 Victorian Spatial Excellence Award for Education and Professional
Development.
Tim Malthus is leader of the Environmental Earth Observation program in CSIRO Land and Water in
Canberra, Australia. His current projects include TERN (Terrestrial Ecosystem Research Network), IMOS
(Integrated Marine Observing System) and the investigation of land use and land cover classification at high
resolution. Tim’s specialization in calibration/validation activities, and field spectroscopy with analysis of
airborne and satellite Earth observation data, is applied in the development of improved monitoring tools for
informing wider environmental policies. He has held positions as Senior Lecturer in Remote Sensing,
University of Edinburgh, 1994–2009 and Director of the NERC Field Spectroscopy Facility, UK, 2004–09.