SDAR data model

SDAR data model

John Ortiz 1,2,3, Carlos Jaramillo 1,2

1 Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama, 2 Corporación Geológica ARES, Bogotá, Colombia. 3 Servicio Geológico Colombiano, Bogotá, Colombia.

SDAR is a fast and consistent tool for plotting and facilitating the analysis of stratigraphic and sedimentological data, designed to plot detailed stratigraphic sections and to perform quantitative stratigraphic analyses.

This document presents the specific types of data required by SDAR package. The representation schemes and standard formats that should be satisfied by the input data set to be integrated on SDAR are mentioned.

Data model

Many of the sedimentological, stratigraphical and paleontological features share common properties. For example, lithology, bioturbation, and lithostratigraphic and chronostratigraphic units are all defined over a stratigraphic range (i.e., each of them has to be defined by a base and a top). Moreover, features as structural data, and geochemical and geochronological analysis, are usually collected, or correspond to a specific stratigraphic position (i.e., each of them represents a unique depth into the well log). On the other hand, other features as fossil occurrences, samples, and sedimentary structures, could be described by both, stratigraphic range, or a specific stratigraphic position (e.g., a fossil occurrence could be presented in a specific depth, throughout a bed, or throughout a set of beds). Therefore, a flexible data model able to store and to integrate all the previous descriptions was implemented. SDAR allows users to provide stratigraphic information in these three main types: beds, intervals and punctual features. A description and an example of each data type are provided below.

NOTE: The SDAR project includes the development of a graphic user interface to connect this R package with a database management system; for this reason the structure of the data and headers (column names) should be followed in order to match the database structure.

beds (data format to integrate rock layers)

A layer of rock is the fundamental unit in an Stratigraphic Columns (SC) representation. It describes the thickness, composition, and texture of a rock. In order to integrate a stratigraphic layer in SDAR, the information required for each layer is bed number, thickness (i.e, it is defined by a base and a top), rock type, primary lithology, and grain size. To improve communication between geoscientists, some conventions, defined by sedimentologists to draw lithology patterns, and to describe grain size and color, are implemented. Details on the information required to define a layer and the sources for the conventions implemented are provided below.

  • bed_number: numeric; It is often useful to give to each bed, or rock unit, a number so as to facilitate later reference; begins at the stratigraphically lowest bed (tucker2011).
  • base and top: numeric; They define the bed thickness of each layer. Overlapping is not allowed between layers.
  • rock_type: string; This field must include only the values listed in Table 1.

Table 1: Rock type

id Rock Type
1 sedimentary
2 volcaniclastic
3 covered
  • prim_litho: string; This field must include only the values listed in Table 2. Primary lithology (To draw lithologic patterns, conventions suggested by the Federal Geographic Data Committee FGDC (fgdc2006) are implemented).

Table 2: Primary lithology

id Lithology
1 claystone 13 coal
2 mudstone 14 gypsum
3 shale 15 halite
4 siltstone 16 chert
5 sandstone 17 glauconite
6 conglomerate 18 limonite
7 breccia 19 siderite
8 limestone 20 phosphorite
9 dolostone 21 tuff
10 marl 22 lapillistone
11 chalk 23 agglomerate
12 diatomite 24 bentonite
  • grain_size: string; This field must include only the values listed in Table 3. The conventions are based on the Wentworth classification system for siliciclastic rocks (wentworth 1922), for pyroclastic rocks (wentworth 1932), and for classification of carbonate rocks (dunham 1962) are implemented.

Table 3: Grain size table

id Grain Size
1 clay 22 mudstone
2 clay / silt 23 wackestone
3 silt 24 packstone
4 silt / very fine sand 25 grainstone
5 very fine sand 26 floatstone
6 very fine / fine sand 27 rudstone
7 fine sand 28 boundstone
8 fine / medium sand 29 framestone
9 medium sand 30 bindstone
10 medium / coarse sand 31 bafflestone
11 coarse sand 32 crystalline
12 coarse / very coarse sand 33 fine ash
13 very coarse sand 34 medium ash
14 very coarse / granule 35 coarse ash
15 granule 36 very coarse ash
16 granule / pebble 37 fine lapilli
17 pebble 38 medium lapilli
18 pebble / cobble 39 coarse lapilli
19 cobble 40 fine blocks and bombs
20 cobble / boulder 41 coarse blocks and bombs
21 boulder

In summary, a table with the structure presented in table 4 must be provided. Each row in this data array describes a stratigraphic bed/layer. This example is from a borehole core where depths are measured down from the surface, therefore “base” is greather than “top”.

Table 4: Example of beds/layers table.

bed_number base top rock_type prim_litho grain_size
1 671 670.2 sedimentary claystone clay
2 670.2 669.4 covered
3 669.4 669.18 sedimentary sandstone medium sand
4 669.18 667.6 sedimentary limestone wackestone
5 667.6 667.2 sedimentary conglomerate boulder
6 667.2 666.2 sedimentary shale silt

We have provided on the SDAR repositoy a template of the data format used by SDAR as a Microsoft Excel spreadsheet, SDAR_v0.95_beds_template.xlsx. This is the suggested format by SDAR to store thickness, and texture description of rock layers (beds).

  • The fields “bed_number”, “base”, “top”, “rock_type”, prim_litho” and “grain_size” must be provided to draw a stratigraphic column on SDAR.
  • The fields “grading”, “grain_size_base”, “grain_size_top”, “munsell_color” and “Rcolor” are optional fields, if any of these optional fields are provided, SDAR will incorporate it on the graphical output.
  • The fields “base_contact” and “notes” are included on the template, but the current version is not able to display it on the graphical output, we are working on making it available in the next version.
  • The fields “prim_litho_percent”, “sec_litho”, “grain_size_sec_litho”, “sec_litho_percent” are included on the template in order to store information for mixed rocks, current version of SDAR is not able to display patterns for mixed rocks yet, but we encourage user to store it.
  • The fields “sorting”, “roundness”, “matrix”, “cement” and “fabric” are included on the template to store texture description of rock layers, this information is not display on the graphical output.

Optional fields

  • grading: string; This field must include only the values listed in Table 5. Grading commonly consists of an upward decrease in grain size (normal grading), however, certain sedimentary process result in an upward increase in grain size (inverse grading).

Table 5: Grading

id Grading
1 normal
2 inverse

  • grain_size_base and grain_size_top: string; These fields must include only the values listed in Table 3. When grading is normal or inverse, the grain size of the base and top must be provided.

  • munsell_color: string; This field must include only the values listed in Table 6. It uses color description based on the Munsell chart codes from the Geological Society of America Rock Color Chart (Committee 1991).

Table 6: Munsell Colors

id Munsell Color
1 5R 8/2 30 10YR 8/6 59 10GY 3/2 88 5B 9/1
2 5R 7/4 31 10YR 7/4 60 5G 7/2 89 5G 8/1
3 5R 6/2 32 10YR 6/2 61 5G 7/4 90 5GY 8/1
4 5R 6/6 33 10YR 6/6 62 5G 6/6 91 5Y 8/1
5 5R 5/4 34 10YR 5/4 63 5G 5/2 92 5YR 8/1
6 5R 4/2 35 10YR 4/2 64 5G 5/6 93 5B 7/1
7 5R 4/6 36 10YR 2/2 65 5G 3/2 94 5YR 6/1
8 5R 3/4 37 5Y 8/4 66 10G 8/2 95 5Y 6/1
9 5R 2/2 38 5Y 7/2 67 10G 6/2 96 5G 6/1
10 5R 2/6 39 5Y 7/6 68 10G 4/2 97 5GY 6/1
11 10R 8/2 40 5Y 6/4 69 5BG 7/2 98 5B 5/1
12 10R 7/4 41 5Y 5/2 70 5BG 6/6 99 5G 4/1
13 10R 6/2 42 5Y 5/6 71 5BG 5/2 100 5GY 4/1
14 10R 6/6 43 5Y 4/4 72 5BG 4/6 101 5Y 4/1
15 10R 5/4 44 5Y 3/2 73 5BG 3/2 102 5YR 4/1
16 10R 4/2 45 10Y 8/2 74 5B 8/2 103 5G 2/1
17 10R 4/6 46 10Y 7/4 75 5B 7/6 104 5GY 2/1
18 10R 3/4 47 10Y 6/2 76 5B 6/2 105 5Y 2/1
19 10R 2/2 48 10Y 6/6 77 5B 5/6 106 5YR 2/1
20 5YR 8/4 49 10Y 5/4 78 5PB 7/2 107 N9
21 5YR 7/2 50 10Y 4/2 79 5PB 5/2 108 N8
22 5YR 6/4 51 5GY 7/2 80 5PB 3/2 109 N7
23 5YR 5/2 52 5GY 7/4 81 5P 6/2 110 N6
24 5YR 5/6 53 5GY 5/2 82 5P 4/2 111 N5
25 5YR 4/4 54 5GY 3/2 83 5P 2/2 112 N4
26 5YR 3/2 55 10GY 7/2 84 5RP 8/2 113 N3
27 5YR 3/4 56 10GY 6/4 85 5RP 6/2 114 N2
28 5YR 2/2 57 10GY 5/2 86 5RP 4/2 115 N1
29 10YR 8/2 58 10GY 4/4 87 5RP 2/2
  • Rcolor: string; Any color name valid in R format (colors function from grDevices package provide a complete list of colors available in R). Instead of using a color name, color can also be defined with a hexadecimal value. Examples are provided on Table 7

Table 7: Examples of R colors

id Rcolor example
1 goldenrod
2 seagreen
3 deepskyblue
4 #8968CD
5 #E9967A
  • base_contact: string; This field must include only the values listed in Table 8. The nature of the boundary at the base of the layer. Base contact is included on the template, but the current version is not able to display it on the graphical output, we are working on making it available in the next version.

Table 8: Base contact

id Base contact
1 sharp planar
2 gradational
3 faulted
4 covered
  • notes: string; Additional description in a free text format, maximum 200 characters by bed (’Comments/Remarks’). Notes is included on the template, but the current version is not able to display it on the graphical output, we are working on making it available in the next version.

Mixed rocks

  • sec_litho: string; Secondary lithology, this field must include only the values listed in Table 2.
  • grain_size_sec_litho: string; Grain size of secondary lithology, this field must include only the values listed in Table 3.
  • prim_litho_percent and sec_litho_percent: numeric; Percent composition of primary and secondary lithology.
  • Note: The fields “prim_litho_percent”, “sec_litho”, “grain_size_sec_litho”, “sec_litho_percent”* are included on the template in order to store information for mixed rocks, current version of SDAR is not able to display patterns for mixed rocks yet, but we encourage user to store it.

Texture description

  • sorting: string; This field must include only the values listed in Table 9. Description of the degree of uniformity of grain size.

Table 9: Sorting

id Sorting
1 very well sorted
2 well sorted
3 moderately sorted
4 poorly sorted
5 very poorly sorted
  • roundness: string; This field must include only the values listed in Table 10. Measurement of roundness of sedimentary particles (Krumbein 1941).

Table 10: Roundness

id Roudness
1 very angular
2 angular
3 sub angular
4 sub rounded
5 rounded
6 well rounded
  • matrix: string; This field must include only the values listed in Table 11. Composition of material wherein larger grains, crystals or clasts are embedded.

Table 11: Matrix

id Matrix
1 muddy
2 sandy
3 ashy
4 micrite
5 not recognizable
  • cement: string; This field must include only the values listed in Table 12. Composition of the crystalline material precipitated around the edges of grains.

Table 12: Cement

id Cement
1 siliceous
2 ferruginous
3 calcite
4 dolomite
5 kaolinitic
6 sparite
7 not recognizable
  • fabric: string; This field must include only the values listed in Table 13. Grain fabric (packing).

Table 13: Fabric

id Fabric
1 clast supported
2 matrix supported

Note: The fields “sorting”, “roundness”, “matrix”, “cement” and “fabric”* are included on the template to store texture description of rock layers, this information is not display on the graphical output.  

Interval features

An interval is defined over a stratigraphic range; it has to be defined by a base and a top. The main requirement to set an interval is that the recorded geological feature (e.g., sedimentary structures, bioturbation, unit name, fossil content) is presented throughout the defined stratigraphic range. Furthermore, users can define an interval by the stratigraphic thickness contained into a given bed. For example; if bioturbation is present just in the top of the bed, users could define the base and top of the bioturbed interval and store it in this format. Following this approach users can store in this format the following features:

  • core number
  • samples
  • visual oil stain
  • bioturbation
  • sedimentary structures
  • fossils
  • other symbols
  • lithostratigraphic frame
  • chronostratigraphic frame

In the data structure to define intervals, the user must define a stratigraphical base, top, and the recorded feature of each interval as is presented in Table 14. Each row in this data array describes a stratigraphic interval with the geological feature described on it. In some interval features overlapping is allowed (e.g., fossils, samples).

Table 14: Example of intervals table (sedimentary structures).

base top sed_structure
671 670.2 cross bedding
671.5 671.5 climbing ripples
669.4 669.18 lenticular lamination
668.2 667.6 normal grading
667.2 666.2 wavy lamination

We have provided on the SDAR repositoy a template of intervals data format used by SDAR as a Microsoft Excel spreadsheet, SDAR_v0.95_intervals_template.xlsx. This is the suggested format by SDAR to store fossils, sedimentary structures, bioturbation, etc. (intervals).

In summary, a table with the structure presented in table 14 must be provided for each recorder feature. The possible values admitted by each geological feature are presented in tables 15-22. The names of the columns must to be called as is presented in each reference table.

  • samples: string; This field must include only the values listed in Table 15.

Table 15: Samples

id Sample Type Default symbol - pch Default color
1 rock sample 15
2 fossil sample 16
3 foraminifera 17
4 geochemistry 18
5 palynology 8
6 petrography 9
7 petrophysics 7
8 XRD 11
  • oil.stain: string; This field must include only the values listed in Table 16.

Table 16: Visual Oil Stain

id Intensity color
1 weak
2 moderate weak
3 moderate
4 moderate strong
5 strong
  • bioturbation: string; This field must include only the values listed in Table 17.

Table 17: Bioturbation

id Index
1 sparse
2 low
3 moderate
4 high
5 intense
6 complete
  • sed.structures: string; This field must include only the values listed in Table 18.

Table 18: Sedimentary Structures

id Sedimentary Structures
1 masive 21 ball and pillow
2 planar lamination 22 convolute bedding
3 horizontal bedding 23 dish and pillar
4 normal grading 24 evaporite molds
5 inverse grading 25 flame structures
6 cross bedding 26 flute casts
7 festoon cross bedding 27 groove cast
8 herringbone cross bedding 28 hardground
9 hummocky cross bedding 29 load cast
10 planar cross bedding 30 mudcrack
11 through cross bedding 31 pseudo nodules
12 swaley cross bedding 32 tool marks
13 ripple lamination 33 rain prints
14 climbing ripples 34 slump structures
15 current ripple cross lamination 35 syneresis cracks
16 wave ripple cross lamination 36 mottling
17 flaser lamination 37 peds
18 heterolithic lamination 38 rooting
19 lenticular lamination 39 slickensides
20 wavy lamination
  • fossils: string; This field must include only the values listed in Table 19.

Table 19: Fossils

id Fossils
1 macrofossils 30 reptiles
2 invertebrates 31 plants
3 annelids 32 leaves
4 arthropods 33 roots
5 arachnids 34 wood
6 crustaceans 35 algae
7 insects 36 conifers
8 trilobites 37 ferns
9 brachiopods 38 flowering plants
10 bryozoans 39 stromatolites
11 cnidarians 40 fungi
12 corals 41 microfossils
13 stromatoporoids 42 conodontss
14 echinoderms 43 diatoms
15 crinoids 44 foraminifera
16 echinoids 45 larger foraminifera
17 graptolites 46 benthonic foraminifera
18 mollusks 47 planktonic foraminifera
19 cephalopods 48 nannofossils
20 ammonoids 49 ostracodes
21 belemnoids 50 palynomorphs
22 nautiloid 51 acritarchs
23 gastropods 52 chitinozoans
24 bivalves 53 dinoflagellates
25 sponges 54 pollen spores
26 vertebrates 55 radiolarians
27 amphibians 56 silicoflagellates
28 fish 57 spicules
29 mammals
  • other.sym: string; This field must include only the values listed in Table 20.

Table 20: other symbols

id Other Symbols
1 concretions 9 kaolinite
2 nodules 10 mica
3 intraclasts 11 olivine
4 stylolites 12 organic matter
5 calcite 13 pyrite
6 feldspar 14 pyroxene
7 glauconite 15 siderite
8 gypsum 16 sulphur
  • lithostrat: string; This field must include only the values listed in Table 21.

Table 21: Lithostratigraphic Ranks

id Litho Unit Rank
1 group
2 formation
3 member
  • chronostrat: string; This field must include only the values listed in Table 22.

Table 22: Chronostratigraphic Units

id Chrono Unit
1 super_eonothem
2 eonothem
3 erathem
4 system
5 series
6 series_subseries
7 stage

Acknowledgments

This project has been sponsored by Carlos Jaramillo (Smithsonian Tropical Research Institute), financial support of this research was provided by COLCIENCIAS (partly funding the master studies of the main author) fundación para la Investigación de la Ciencia y la Tecnológia del Banco de la República, (Colombia), Corporación Geológica ARES (Colombia), and the Smithsonian Tropical Research Institute, the Anders Foundation, 1923 Fund and Gregory D. and Jennifer Walston Johnson.

The Saltarin 1A well dataset for this analysis, was provided by Alejandro Mora of HOCOL S.A.

Bibliography