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Frequently Asked Questions (FAQs) about dbSEABED

FAQs in PDF format

dbSEABED

What is dbSEABED?
What kind of outputs does dbSEABED produce?
What quality-control measures are in place for dbSEABED?

Output files

What is the source (SRC) file output?
What is the function of the output component (CMP) and facies (FAC) files?
What is the CMP file output for?
What is the meaning of the data in the facies (FAC) output file?
What do all the "-99"'s mean?
Why are there negative values for seabed strength and critical shear strength?
Compared to values given in some scientific papers, the output values from dbSEABED are quite rounded. Why?
What is the "Rock" membership?
What is the meaning of the SeaBedClass and ClassMembership?
What is the "Weed" membership?
Hydrographic Bottom Type (HBT) codes can be output. What do they mean?
What does the Roughness code mean?
Why do some points plot on the land?
Can the same sample or analysis be represented more than once in the data collection?
Why are the kurtosis and skewness not reported from the database?

Linguistic data versus numeric data

How does dbSEABED make text data conformable with numerical data?
What if a user doesn't want to use the word-based data for mappings?
Which form of data should I trust more, numeric-value analyses or word-based descriptions?
How do text-based descriptive data relate to numeric-value analytical data?

Grain size

Why are values of grain size only given to one decimal place, whereas percent sand, and other data are given as integers?
How are the grain sizes extracted from data?
Are detailed grain-size analyses used to output textural statistics, such as mean and sorting?
Why would a sample that is known to have had a detailed grain-size analysis not appear in the output data?
How are the outputs for the grain-size fractions of gravel, sand, and mud extracted?
Are grain-size scales other than Wentworth used?
How is one central grain size recovered from diverse data that may present mean, median, and other graphical grain sizes?
How are the central grain size and sorting estimated in the calculated (CLC) process of the database?

Data processing methods

What is fuzzy logic and how does it work?
What is the method of attributing subbottom depths to samples from cores?
How are the shear strengths derived?
What is the method for arriving at the Shepard and Folk classes?
What relationships are used to estimate critical shear stress values?
How are the porosity values obtained?
What is the basis for the data on compressional (p-wave) sound speeds?
How are the sorting values determined?
How are carbonate and organic carbon values determined?

Data import methods

How does dbSEABED hold the basic data?
Why does dbSEABED hold its underlying data in documents rather than a relational database like Oracle™*?
What is involved in importing datasets into dbSEABED?
How are metadata treated?
Why are sediment descriptions and biological names held as abbreviations?

Color
Where can I find more information on the Munsell color code?
How are the Munsell color codes derived?

How to
How can I map the coded information on color and roughness in a GIS?
How can I use the critical shear stress in a practical application?

dbSEABED

What is dbSEABED? [top]

What kind of outputs does dbSEABED produce? [top]

What quality-control measures are in place for dbSEABED? [top]

Quality control is practiced at many stages in dbSEABED:

As each new data set is entered, it is tested in programs of dbSEABED to seek errors, and so on. The program detections of problems are highlighted on screens during run time and are also reported to logs. As errors are detected, edits are made in the structured data files, complete with metadata explaining the edits. In some cases data will be deactivated (flagged out), again with metadata explaining the process.


Output files

What is the source file (SRC) output? [top]

The source file (SRC) gives basic information on the survey and data set that a sample belongs to, such as the collector and institution, confidentialities, number of samples, dates, and region.

What is the function of the output component (CMP) and facies (FAC) files? [top]

What is the component (CMP) file output for? [top]

What is the meaning of the data in the facies (FAC) output file? [top]

Once the memberships (abundances) of components are calculated, they can be combined into an assessment of the membership a sample shows to a range of sedimentary, rock, or ecologic facies. Each facies is typified by components Af,Bf,... with memberships af,bf,..., for example, a CalcareousPelagic facies as

"pfrm nan ptr cal_ooz ; 1 1 1 1 0 0".

The components are senior synonyms from the parsing dictionary. Given a set of components in a sample As,Bs,... with memberships as,bs,..., the sample membership of each facies is calculated as

MIN(ac,af)+MIN(bc,bf)+...

for each case of a coinciding component. In fuzzy-set theory this is a set intersection - an "AND". See tables 4 and 5 in this publication for lists of components and facies, respectively.

Of course, the facies output is possible only from the parsed word-based data. Because not all studies report grain components, it is advisable to plot these results as point symbols only, not areal griddings.

What do all the "-99"'s mean? [top]

Why are there negative values for seabed strength and critical shear strength? [top]

These parameters are given in terms of their logarithm (base 10). A negative value implies a strength or shear stress less than 1.

Compared to values given in some scientific papers, the output values from dbSEABED are quite rounded. Why? [top]

Studies of uncertainty show that accuracies on most sediment parameters are of order 1 to 3 percent of the total parameter range even under favorable laboratory conditions. The significant figures in dbSEABED outputs reflect the observed uncertainties.

What is the "Rock" membership? [top]

What is the meaning of the SeaBedClass and ClassMembership? [top]

These columns list the facies showing the largest membership value for each sample, and the value of the membership. The memberships are calculated as described on this page about the facies (FAC) file. Output occurs only provided that the membership is greater than or equal to 0.33. Of course, this output is possible only from the parsed word-based data.

What is the "Weed" Membership? [top]

Hydrographic Bottom Type (HBT) codes can be output. What do they mean? [top]

Note: Data for Hydrographic Bottom Type have not been included in this publication.

What does the Roughness code mean? [top]

Why do some points plot on land? [top]

Some source data collections contain data in estuaries, rivers, and lakes; others contain data for coastal dunes, beaches, and even coal mine pits. Sites that are clearly located in error are decommissioned in the data resources files (DRF), but data are kept that known to be on the beach, in rivers, estuaries, and lakes, or are known to be properly located on land..

Can the same sample or analysis be represented more than once in the data collection? [top]

Yes, when there is a good reason. For instance, the same sample may be described by two different labs or be reanalyzed years later, or an analysis may be expressed in a different way by later work. These double-up results are all valid and should be included in the database for mapping. (Note that the duplicate analyses may not carry exactly the same sample names.) The USGS attempts to remove obvious data overlaps, choosing the original data, where available, over derived data, which are often held in pre-existing data compilations. An example of this is the National Geophysics Data Center (NGDC) compilation, Deck 41.

Why are the kurtosis and skewness not reported from the database? [top]

These higher order moments are not only rarer in data sets, but to be accurately reported require a higher standard of data and calculation than lower moments. Statistical moment and graphical measures are also very difficult to reconcile, exacerbating the shortage of available data on which to base outputs.


Linguistic data versus numeric data

How does dbSEABED make text data conformable with numerical data? [top]

What if a user doesn't want to use the text-based data for mappings? [top]

Users have a choice, if only numerical analytical data are required, then the extracted (EXT) form of output should be used; if text data only, then the parsed (PRS) form should be used. Some users will not want to use the calculated (CLC) outputs, which have a higher level of uncertainty than these, which is also possible. If a user wants to integrate these to achieve the best possible coverage in a region, then they can be added or telescoped together using two other formats (ALL and ONE formats, respectively; not included in this publication).

Which form of data should I trust more, numeric-value analyses or text-based descriptions? [top]

There are several issues that users must consider in deciding which form of data to use:

How do text-based descriptive data relate to numeric-value analytical data? [top]


Grain size

Why are values of grain size only given to 1 decimal place whereas percent sand and other data are only given as integers? [top]

Work in the dbSEABED project has established the typical accuracies on measurements of these parameters. Those accuracies, even for careful work, are of the order of 2 to 5 percent of half the total range of the parameter. The table outputs are designed to be brief to restrict data volumes and make mapping faster and easier and to carry the data at a precision that is appropriate to measurement accuracies.

How are the grain sizes extracted from data? [top]

By a simple reporting of the average grain size, median grain size, Inman (1952) mean and Folk (1954) graphic mean grain sizes. A comparison of data sets shows that these reflections of "central" grain size are not significantly different within usual error bounds on sampling then analysis. (On the other hand, sorting values are significantly different and cannot be combined in the same way.)

Are detailed grain-size analyses used to output textural statistics such as mean and sorting? [top]

Why would a sample that is known to have had a detailed grain-size analysis not appear in the output data? [top]

Grain-size analyses are scanned to check that they are in good order, and some are rejected. An analysis with any phi interval is acceptable, provided it is detailed enough to resolve particular fractions. Analyses that have a significant weight percent in the finest and coarsest classes are treated as suspect because this implies that the part of the sediment that was analyzed probably does not represent the whole sediment.

How are the outputs for the grain-size fractions of gravel, sand, and mud extracted? [top]

Many data sets contain these values (based on Wentworth scale), and in those cases, the values are passed through to extracted (EXT) output. In some cases the data are presented in the form of a detailed grain-size analysis — such as at 1/2 phi intervals. dbSEABED assembles grain size analysis streams into G:S:M fractions by assigning each analysis class to its fraction (or proportioning if the class straddles a fraction boundary).

Note: Many grain size analyses techniques range only through sand and mud, while gravel is not analysed. In these cases the database reports the gravel percent as null in outputs.

Are grain-size scales other than Wentworth used? [top]

Generally no. However, an option does exist for users to report percent mud from values of "engineering" grain size mud (that is, finer than No. 200 Sieve, 75µm).

How is one central grain size recovered from diverse data that may present mean, median, and other graphical grain sizes? [top]

The database adopts mean moment grain size as the standard for its measure of a sediment's central grain size. Studies show that the median, Inman (1952) "mean", and Folk (1954) "mean" grain sizes fit this quite well for a wide variety of sediments. However, mode grain sizes do not, and are not included in "central grain size."

How are the central grain size and sorting estimated in the calculated (CLC) process of the database? [top]


Data-processing methods

What is fuzzy logic and how does it work? [top]

"Fuzzy logic" (more properly "fuzzy set theory" or FST) allows an object to belong partially to a set. In classical "crisp" set theory objects are either in a set or not. FST suits words because they are often partial carriers of meaning. For example, "warm" is partially hot and partially cold. A formal arithmetic for fuzzy sets was discovered by Zadeh (1965). A good reference is Mott and others (1986).

What is the method of attributing subbottom depths to samples from cores? [top]

Ideally, a sample from a core will have a subbottom depth assigned in terms of meters below the sediment surface. However, this is not always the case. Although this information may have to be left unknown if not given by the original researchers, some limits can be placed if the sampler type is known. For example a Shipek grab sampler usually has only 5 cm of penetration. Then a subbottom range of 0-0.05 m can be assigned. In cores that may be several meters long, the limitation is less strict.

How are the shear strengths derived? [top]

Shear-strength values are obtained either from actual measurements held in the database or are assessed from descriptions that convey lithification or consolidation.

What is the method for arriving at the Shepard and Folk classes? [top]

The original Shepard (1954) and Folk (1954) ternary classifications had to be modified in a couple of ways for use by dbSEABED: (a) where the silt and clay breakdown of mud is not available, the silt-clay domains in the classifications are merged under one name; and (b) because these schemes refer only to sediments, an extra class "solid" is added for dbSEABED to classify all lithified materials (rock). The aim of (a) is to have a class attached to a greater number of samples. Very few samples in the database have the silt:clay ratio specified.

What relations are used to estimate the critical shear stress values? [top]

Depending on the quality of inputs and nature of the sediment, several relations are used to predict critical shear stresses (CSS). The details and supporting references are given in the onCALCULATION document. The relationships include:

No regard to the effects of bioconsolidation or bioturbation is made.

How are the porosity values obtained? [top]

What is the basis for the data on compressional (p-wave) sound speeds? [top]

Although there are some direct measurements of compressional sound speeds for areas of the seabed, they are few and far between. dbSEABED reports any direct measurements in the extracted (EXT) outputs, including the average of those data that recognize velocity anisotropy. One difficulty with sound speeds is that they do depend on the frequency, pressure, and temperature of the measurement. The outputs make no allowance for these factors, though conditions of the original measurements are recorded in the underlying raw data of the database.

Several users of dbSEABED requested that estimated sound speeds be provided wherever possible. This is done as follows.

How are the sorting values determined? [top]

Values of moment sorting are simply passed through to output. Graphical measures of sorting, such as those of Inman (1952) and Folk (1954), are not generally compatible with moment measures and at present do not contribute to outputs.

How are carbonate and organic carbon-values determined? [top]


Data-import methods

How does dbSEABED hold the basic data? [top]

Datasets for processing are held in structured documents that are called "Data Resource Files" (DRF). They set out data in the form of a written geological core log, in a tree structure that nests the data according to expedition, the sample site, the sample, and finally phase inside the material. dbSeabed programs process the data held in this format to produce Geographic Information Systems (GIS) and Relational Data Base (RDB) -compatible formats.

Why does dbSEABED hold its underlying data in documents rather than a relational database like Oracle™*? [top]

This is one of the most successful features of dbSEABED.

What is involved in importing data sets into dbSEABED? [top]

How are metadata treated? [top]

Why are sediment descriptions and biological names held as abbreviations? [top]

To make the parsing (and dictionary lookup) computationally faster, to make long descriptions shorter and more readable, to give flexibility in handling homonyms, and to better distinguish active data from metadata in the structured documents.


Color

Where can I find more information on the Munsell color code? [top]

Refer to the Geological Society of America "Color Rock Chart," or to the company GretagMacbeth, which is the modern-day custodian of Munsell's color technologies.

How are the Munsell color codes derived? [top]

This process is fully described in Jenkins (2002). Munsell codes are explained in a publication of the Geological Society of America (Goddard and others, 1951). The essential steps in the treatment of color data are as follows:


How to

How can I map the coded information on color and roughness in a GIS? [top]

How can I use the critical shear stress (CSS) in a practical application? [top]

The critical shear stress (CSS) and grain size are essential components for calculating the Shields criterion of sediment erosion, between the Shields Parameter and the Grain Reynolds Number. Those parameters can be calculated once the flow characteristics, fluid velocities, densities, and other factors are known. See standard textbooks on sediment erosion for more information (for example, Soulsby, 1997).

Selected References

Blatt, H., Middleton, G.V., and Murray, R.C., 1980, Origin of sedimentary rocks (2d ed.): Prentice-Hall, Inc., 782 p.

British Admiralty, 1973, Chart 5011: Symbols and abbreviations used on Admiralty Charts (new series): Taunton, UK, The British Hydrographic Office, Taunton, UK.

Folk, R.L., 1954, The distinction between grain size and mineral composition in sedimentary rock nomenclature: Journal of Geology, v. 62 no. 4, p. 344-359.

Folk, R.L., 1974, The petrology of sedimentary rocks: Austin, Tex., Hemphill Publishing Co., 182 p.

Goddard, E.N., Trask, P.D., de Ford, R.K., Rove, O.N., Singewald, J.T., and Overbeck, R.M., 1951, Rock Color Chart: Boulder, Colo., Geological Society of America.

Inman, D.L., 1952, Measures for describing the size distribution of sediments, Journal of Sedimentary Petrology, v. 22, p. 125-145.

Jenkins, C.J., 2002, Automated digital mapping of geological colour descriptions: Geo-Marine Letters, v. 22, no. 4, p 181-187.

Mott, J.L., Kandel, A., and Baker, T.P., 1986, Discrete mathematics for computer scientists and mathematicians (2d ed.): Reston, VA, Reston Publishing Company, 751 p.

Nafe, J.E., and Drake, C.L., 1960, Physical properties of marine sediments, in Hill, M.N. (ed.), The Sea, v. 3, New York, Wiley, p. 794-815.

Richardson, M.D., and Briggs, K.B., 1993, On the use of acoustic impedance values to determine sediment properties: Proceedings Institute Acoustics, v. 15, p. 15-24.

Shepard, F.P., 1954, Nomenclature based on sand-silt-clay ratios: Journal of Sedimentary Petrology, v. 24, p. 151-158.

Soulsby, R., 1997, Dynamics of marine sands: London, Thomas Telford, 249 p.

Zadeh, L.A., 1965, Fuzzy sets: Information and control, v. 8, p. 338-353.

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*Any use of trade names is for descriptive purposes only and does not imply endorsement by the U.S. Government.


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