Catalog Manager application

The Catalog Manager (CM) application provides a save and structured way for GEODESC support staff with the reviewer role to edit the GEODESC catalogs

Catalog templates

Catalog templates are created and maintained by the operators of the GEODESC applications using the Catalog Manager application. Their design is based on years and decades of core description experience on the JOIDES Resolution. Their purpose is to kick-start the collection of project templates ultimately used for data capture in a project. All catalog templates share the parameters in Table <catalog template parameters>. Refer to the project templates for an expanded set of parameters used in the project-specific templates.

Table <catalog template parameters>.

Database notationDatabase formatUser interface labelDescription
SCALEVARCHAR2 (50 BYTE)ScaleSee Template.

Large sample types

Small sample types

See Sample groups.
SAMPLE_TYPESVARCHAR2 (4000 BYTE)Sample typesSee Sample types.
HEADER_HEIGHTNUMBER (38)Header row heightDefault header row heigh for a template.
ROW_HEIGHTNUMBER (38)Data row heightDefault row heigh for all data rows in a template.

Data Access application

The Data Access application is a publicly available tool to download all existing GEODESC data. This includes descriptive data files by hole, metadata files by project, and current catalog contents used in templates. Users need to sign in with valid credentials to access project data under moratorium.

Data Capture application

The Data Capture application is a spreadsheet tool used to capture core description and micropaleontological observations. The spreadsheet looks and feels similar to generic spreadsheet programs, however, is is highly customized for effective and efficient collaborative workflows as customary on the scientific ocean drilling vessel JOIDES Resolution. Functionality is in many ways enhanced with special features specific to the workflow requirements, and it is also in many ways restricted in regard to generic spreadsheet functions to ensure data integrity.

Users with the observer role credentials create worksets on the capture sheet dashboard and open them into data capture worksheets. Users then enter their observations in the feature-rich worksheets, which are autosaved in real time, but not available outside the Data Capture application until users publish the worksheet/workset. Published data are publicly available as tab-separated values (TSV) formatted text files using the Data Access application.

Data capture worksheet

A data capture worksheet is the instantiation of a workset and allows users with the observer role to enter, edit, and save observations.

Datum catalog

The datum catalog contains all formal datums, by microfossil group, and with ages from all relevant, published time scales/ages, so the datums and ages can be associated with micropaleonological observations. Using the Template Manager application, template makers can add a datum column to a template and select:

  • the times scale(s) (ages) to be added to the template as separate columns, and
  • the datums to be presented in a dropdown list in the Data Capture application.

Datum catalog table 1. The datum catalog has three basic parameter columns, and an additonal number time scale (age) columns that may grow with time whenever a new time scale is published.

Parameter columnsParameter description
Microfossil groupA single number series for all zones of all zonal schemes in the GEODESC catalog.
Datum type
Sort order
<Time scale 1>
<Time scale 2>


Description interval

A description interval is a layer within the stratigraphic sequence, defined for a discrete set of observations. Within large sample types, the observer defines the description interval with an Offset top and an Offset bottom in cm from the top of the section, based on material changes in texture, composition or structure, or as a predefined, regular interval (e.g., every 10 cm). Description intervals for small sample types (e.g., a thin section) are defined and registered at the time the sample is taken. A description interval can represent the scope of description, but not all scopes of description are intervals (e.g., domains).

Descriptive data file

Data files contain the observations made using a template, for a hole. They are created and stored automatically by the GEODESC Data Capture application whenever the observers upload the data in their project worksheet. Data files are exported here as tab-delimited text files for longevity and ease of analysis and visualization. 

The data file has a single header row explaining the meanings of the columns in short form, followed by as many rows as description scopes (samples, sample intervals, domains) specified and used by observers using the template.

The first 18 columns are the scope of description columns (the sample or description interval, with depths). The additional columns are observable columns

Descriptive metadata file

Metadata files contain the template configuration used to record observations in the data capture worksheets. They are created by the GEODESC Template Manager application whenever the template maker last saved a project template. Metadata files are exported here as tab-delimeted text files for longevity and ease of analysis and visualization.

Table Final product metadata file 1. A metadata file as 30 rows for 4 section headers and 26 parameters, and as many columns as the template has columns (plus one column for row headers).

Row no.

Column 1 labelColumn 2 data
1FILE INFORMATION(This section has only this one data column)
2File name:<project_scale_type_objective_extension>
3Template last changed on: <YYYY-MM-DD  hh:mm:ss>
4Template last changed by:<name>
5TEMPLATE SETTINGS(This section has only this one data column)
6Scale:<summary | macroscopic | microscopic>
7Type: <igneous | sediment | structures | micropaleontology | ...>
10Sample group:  <L | S>
11Sample types: <HOLE, CORE, SECT, SHLF-A, SHLF-W, WRND,...>
12WRND sample scopes created automatically:<on | off>
13Section lengths adjusted automatically:<on | off>
14SCOPE COLUMNS(This section has as many columns as the template has scope columns, i.e., 18.)
15Column header:<text>
16Full definition:<text>
17OBSERVABLE COLUMNS(This section has as many columns as the template has observable columns.)
18Column header:<text>
19Full definition:<text>
20Entry type:<1 or 2 words>
21Quantification:<1 or 2 words>
22Texture or appearance:<1 or 2 words>
23Source or state:<1 or 2 words>
24Composition:<1 or 2 words>
25Focus:<1 or 2 words>
26Entry requirement:<on | off>
27Contiguity requirement:<on | off>
28Exclusivity requirement:<on | off>
29Validation type:<text | list (single-select) | list (multi-select) | numeric | formula>

Validation details:

  1. if validation_type=text
  2. if validation_type=list (single-select or multi-select)
  3. if validation_type=numeric
  4. if validation_type=formula

  1. <empty>
  2. <comma-delimited string of list items>
  3. <minimum=# , maximum=# , decimals=#>
  4. <formula string without '='>

Display attributes

GEODESC observables and the resulting worksheet columns have display attributes to make the the data capture workflow more ergonomic and efficient. The display options are limited to those useful during data capture.

Table Display attributes.

ScopeAttributeSetting options
Observable/columnVisibilityon = unhide, off = hide
Lock visibilityon = Data Capture cannot change it, off = no lock
Column widthrecommended values: 20~150
Background colormillions of color
Header cellVertical aligntop, middle, bottom
Horizontal alignleft, center, right

Word wrap

on, off
Orientationhorizontal, vertical
Data cellsVertical aligntop, middle, bottom
Horizontal alignleft, center, right

Word wrap

on, off

The display attributes can be set at 3 levels:

  • Catalog Manager application
    • The settings applied in the catalog by the GEODESC specialists and support people will be the default for observables added to a project template.
  • Template Manager application
    • Project teams can change the default settings of catalog observables in their project templates, and they can set the display options for observables they create within their project templates.
  • Data Capture application 
    • Individual observers can change the Templates Manager default settings for the duration of their data capture session.


Domains are a type of scope of description, represented by data capture worksheet rows. They are part of description intervals, differentiated by numbers.

Domains are useful in core description when instances of the materials are too numerous and/or irregularly shaped, making description of each instance in a separate description interval too tedious or outright impossible. Examples include: many thin alternating layers that can be described summarily, irregular areas (volumes) of different lithologies (particularly in thin sections), populations of clasts or grains as well as the matrix or cement, alteration patches or halos, etc..

All domains in a description interval share the exact same sample identity and Offset top and Offset bottom. Domain numbers are sequential, non-negative integers, starting at 1 for each description interval. The highest domain number therefore also reflects the number of domains in the description interval. Singular description intervals have no domain number. Domain numbers are managed automatically by the Data Capture application and have no relation to the material description. Domain numbers are assigned when users add a domain using the row context menu, or if they edit offsets (large sample types) such that the description interval is exactly the same as an existing one. Domain numbers are removed (and potentially renumbered) when users delete a domain.

Entry controls

Entry requirement rule

The Entry requirement rule may be applied to an observable if each scope must have an observation in that column. Example: in the core summary template each core must have a summary description.

Entry requirement is an observable attribute set in the Template Manager application. Entry requirement can only be enabled for an observable if both the contiguity and exclusivity requirements are disabled.

When a data worksheet is validated, the Data Capture application checks observables for which entry requirement is enabled. If a scope does not have an entry for that observable, the empty cell as well as the relevant scope fields are flagged as invalid.

Contiguity rule (no gap rule)

The contiguity rule may be applied to an observable for which the entire stratigraphic section in a hole must have contiguous observations. Example: For the observable ‘Principal lithology’, all sample intervals must have a lithology assigned. NOTE: if overlaps should also be disallowed, pair this control with the exclusivity rule.

Contiguity is an observable attribute set in the Template Manager application. Contiguity can only be set for an observable if entry requirement rule is disabled. The Template Manager application notifies the user if entry requirement rule is enabled.

When a data worksheet is validated, the Data Capture application checks observables set to be contiguous for gaps. This validation also checks the ‘No material present observable’ column for an entry. If an entry exists (e.g., 'WRND' or 'void' to indicate why a gap in the description exists), that scope will not be counted as a gap. If gaps are present between, above or below description intervals within a section, the relevant offsets as well the observations above and/or below the gap are flagged as invalid.

Exclusivity rule (no overlap rule)

The exclusivity rule may by applied to an observable for which observations must not have stratigraphic overlaps. Example: For the observable ‘Grain size’, no more than one grain size class shall be assigned to any sample interval. A grain size class is exclusive to an interval. NOTE: if gaps should also be disallowed, pair this control with the contiguity rule.

Exclusivity is an observable attribute set in the Template Manager application. Exclusivity can only be set for an observable if the entry requirement rule is disabled. The Template Manager application notifies the user if Entry requirement is enabled.

When a data worksheet is validated, the Data Capture application checks observables set to be exclusive for stratigraphic overlaps and flags any overlapping observations as well as the relevant offsets as invalid.

Entry validation types

Observable columns have an attribute 'entry validation type'. This setting determines what type of observation users can enter in that column, and how the program validates the entries and flags errors. 

  • Text
    • Has no restrictions or validations except for basic text character types.
  • List (single-select)
    • Template makers define a list of allowed values and observers must select one of the values (or none, unless the entry requirement rule or potentially the contiguity rule are enabled).
    • If observers enter a value that is not in the list, the Data Capture application will flag the cell as invalid and the data worksheet cannot be uploaded until the flagged error is fixed.
    • Single-select lists can have rank columns.

  • List (multi-select)
    • In some cases, a template is more conveniently configured in a way where observers can add multiple values from a list into one cell instead of having multiple columns for those entries. This preference is typical when observations apply to few scopes but include many items (e.g., multiple fossils in rare fossiliferous beds, multiple structures in rare beds displaying sedimentary or deformational structures). Only values from the list can be selected.
  • Numeric
    • Template makers can set an observable column to numeric so that only numbers can be entered.
    • Three parameters can be specified in the Template Manager application: maximum, minimum and number of decimals, with defaults set at 360, -360 and 0, respectively.
    • The Data Capture application will flag as invalid any observer entry that is outside the minimum and maximum limits, and round observer entries to the specified number of decimals.
  • Formula
    • Formula type columns are typically used to concatenate observations from other columns (e.g, lithology), sum up percentage estimates to ensure a total of 100% (e.g., constituents in a smear slide), and rotate measured orientations into the core reference framework.
    • Template makers define formulas using other observables as arguments.
    • The Data Capture application will execute the formulas and indicate errors, similar to other spreadsheet programs. Observers cannot edit formula cells within the Data Capture application.

Entry value catalog

The entry value catalog is an inventory of geological and general terms used to create entry validation lists, which are associated with observables of entry validation type list. Entry validation lists appear as a dropdown list in the data capture sheet and observers must use one (or more) of those values. Project teams can modify the value lists and add non-existent ones for their project, using the Template Manager application.

In the catalog, entry validation values are organized into contextual grouping and sort orders. 

GEODESC users have access to the catalog from within the Template Manager application. Template makers can pick from this catalog and make choice lists associated with observables as a means of entry validation and quality control.

General users users can download all or a filtered part of the catalog as a tab-delimited text (*.txt) file using the public Data Access application. This is a way to review the catalog and propose additions or corrections to the GEODESC managers. The value list may also be useful for other projects, including teaching.

Table Entry value catalog 1. Description of the five entry value catalog parameters, presented as columns in the download file. 

Parameter (column)Description
ValueThe geological terms used during data collection, selectable from user-configured dropdown lists in the Data Capture application.

These are mostly from the Glossary of Geology, and from other sources as indicated.

First orderGEODESC hierarchical grouping of entry values. Establishing an up to 3-tier hierarchy of thousands of geological terms is non-trivial. The groupings and group terms are 'GEODESC designer choices' and simply meant to facilitate the discover of conceptually related groups of terms. 
Second order
Third order
Sort orderNumber sequences used to sort contextual sets of entry values.

Expeditions and projects

An expedition is a voyage at sea with one of the vessel platforms employed by the IODP. Expeditions collect samples and acquire data for a project. Whereas traditionally one expedition was carried out for one project, more diverse projects and more dynamic and efficient project management have made it common for multiple expeditions to serve a single project, as well as for a single expedition to serve multiple projects. This concept has not been formalized across the IODP to date, however, the LIMS database (serving the JOIDES Resolution) implemented a formalization. Samples belong to an expedition, and data belong to a project. One practical application is that sample and data moratoriums and other data management tasks are specified for projects, not for expeditions. This affects the GEODESC applications and database as follows:.

  • Samples available for description belong to an expeditions.
  • GEODESC templates used to describe samples, and the data collected with the templates, belong to a project. Each project (whether one or more expeditions) is also a GEODESC project, with its own database and a copy of the most updated catalogs. One practical application is that template modifications made for one project will not affect other projects. Only designated reviewers can update catalog items, using new configuration ideas generated in projects or independent feedback.
  • A projects must be associated with one or more expeditions to have access to the necessary sample registries for description. In most cases, a project is associated with a single expedition. However, if a project revisits a legacy site, re-examines legacy cores, or is planned as a multi-expedition project, the applicable expeditions can all be associated with a project to provide access to those samples.
  • Project and expedition associations are authorized by the Expedition Project Manager(s) and executed by an IT representative.

GEODESC catalogs

GEODESC catalogs are inventories of resources used in creating and editing project templates. The catalogs are available to the template makers in the Template Manager application. Catalog content is managed by GEODESC support personnel using the Catalog Manager application. Anyone can view and download catalog contents using the Data Access application. A detailed description of each catalog can be found at the following locations:


LIMS (or JRSO LIMS) refers to the Laboratory Information Management System (LIMS) implemented by the JOIDES Resolution Science Operator (JRSO) for use on and off the JOIDES Resolution. The LIMS is an Oracle database at its core and the schema is designed for the management of samples, the tests applied to the samples, and the results from these tests. The LIMS was acquired as an out-of-the box commercial product in 2006 and was subsequently customized with business rules that meet the scientific ocean drilling needs.

GEODESC is using the core sample registry in the LIMS as the source for the scopes of description, i.e., only registered samples can be described. This makes GEODESC heavily dependent on the LIMS, which in return offers a lot of features for workflow efficiency and control. Furthermore, GEODESC uses the depth computations implemented in the LIMS and applied to all other types of shipboard measurements on all types of core samples as well.

No material present observable

A special catalog observable with the header and definition ‘No material present’ is available for use with templates for large sample types. The observable is of type ‘list’ and the validation list contains values such as ‘void’, ‘whole-round sample’, etc. If observers select any of these list items for a description scope, any other observation for the scope is flagged as invalid.


An observable defines the objective, or context, of an observation. GEODESC has an observable catalog with hundreds of observables typically used in geological descriptions. Collections of observables used for specific types of materials or features, and/or scales of observations, are referred to as Templates. Project teams can pick existing observables, or create new ones, add them to their project templates, and change their attributes as needed using the Template Manager application. Observables are presented as columns in the data capture worksheet of the Data Capture application

Observables (or columns) consist of:

  • Observable definition
  • Header (a short version of the definition suitable as a column header)
  • Entry controls
  • Display attributes

It has an observable definition and 16 attributes described .

Observable catalog

The observable catalog is an inventory of all observables used in catalog templates so they can be added to any template. Catalog observable records can be downloaded using the Data Access application

Table Observable catalog 1. Observable attributes and their default values. Template makers can change the attribute settings.

Observable attribute groupNo.Observable attributeDefault value for newly created observable columnsDefault value for taxa columns when created in Template Manager
Name and full definition


Headeruser definedfrom taxa list, optionally abbreviated
2Definitionconcatenation of definition keysfrom taxa list
Definition keys

3Entry typeuser selectedn/a
4Quantificationuser selectedn/a
5Texture or appearanceuser selectedn/a
6Source or stateuser selectedn/a
7Compositionuser selectedn/a
8Focususer selectedn/a
Entry controls


Entry requirement



10Contiguity requirementoffoff
11Exclusivity requirementoffoff
12Entry validation typetextlist
13Validation details
  • if entry type = text, nothing.
  • if entry type = list, an array with strings of comma delimited values
  • if entry type = numeric, a string of 3 comma delimited values, e.g.: Minimum: 1.4; Maximum: 2.9; Number of decimal places = 1'
  • if Entry type = formula, the formula string.
  • if entry type = text, nothing.
  • if entry type = list, an array with strings of comma delimited values
  • if entry type = numeric, a string of 3 comma delimited values, e.g.: 'Minimum: 1.4; Maximum: 2.9; Number of decimal places: 1'
  • if Entry type = formula, the formula string.
Column settings

15Lock visibilityoffoff
16Column width10030
17Background colornonenone
Header cell display settings18Vertical alignmiddlemiddle
19Horizontal alignleftleft
20Word wraponon
Data cell display settings22Vertical alignmiddlemiddle
23Horizontal alignleftleft
24Word wraponon
Optional annotation in project (not in catalog)

Observable definition

GEODESC observable definitions ensure that observer entries are captured against a consistently defined context, using fully and correctly spelled scientific terms suitable for data analysis.

Observables are defined differently for core description and for micropaleontology, and the Template Manager application leads the user through the respective processes.

Core description

The definitions use an empirical syntax consisting of 6 concepts, each with a 2-level hierarchy of qualifier words to chose from when creating an observable. This results in a unique set of terms defining the meaning of the observation as well as a decent English sentence. The qualifier words are accessible from within the Template Manager application and can be downloaded using the Data Access application. The syntax elements are:

  • Entry type
  • Quantification
  • Texture or appearance
  • Source or state
  • Composition
  • Focus (the constituent, structure, fossil, etc., that is being described)

An observable definition must have at least the entry type and one more element defined. A definition using a qualifier for each of the six syntax elements would be an extremely rare occurrence.

Syntax elementDescription, examples
Entry type

A mandatory word that relates to one of the four respective observable entry validation type:

  • Text type observables: Comment, Description, Summary, etc. 
  • List type observables: Code, Name, Type, etc., for 
  • Numeric type observables: Angle (deg), Count, Dimensions (mm), Percent (%), etc. 
  • Formula type observables: Computed, Concatenated, Formula result, etc. 

An entry type is required for any observable definition. It is capitalized because it forms the beginning of the definition sentence.


An optional word that quantifies the observation:

  • Statistical: average, maximum, minimum, modal, total, etc.
  • Dimensional: degree, extent, intensity, length, thickness, volume, etc.
  • Abundance: abundance, dominant abundance, relative abundance, etc.
  • Orientation: apparent dip direction 1, apparent dip angle 1, etc.
Texture or appearance

An optional word that specifies texture or appearance of an observation:

  • color, habit, irregular, massive, uniform, shape, texture, etc.
  • crystallinity, grain size, grain size class, grain size distribution, vesicularity, etc.
  • clay, silt, sand,...., etc.
  • cryptocrystalline, microcrystalline, fine grained,...., etc.
Source or state

An optional word that specifies the source or state of an observation:

  • general state: fragmentation, primary, original, secondary, generation, preservation, etc.
  • alteration: altered, filled, fresh, etc.
  • deformation, etc.
  •  etc.

An optional word that specifies the composition of the observation:

  • general composition: composition, crystal, lithic, mineralogy, volcanic, etc.
  • mineral group: amphibole, carbonate, chlorite, clay minerals, minerals, oxide, etc.
  • mineral: clinopyroxene, epidote replacing plagioclase, olivine, orthopyroxene, plagioclase, etc.
  • carbonaceous: organic matter, charcoal or coal, etc.
  • microfossil group: calcareous nannofossils, diatoms, radiolarians, etc.

An optional word that specifies the focus of the observation:

  • general focus: hole, core,  section, interval, domain, etc.
  • lithology components: lithology prefix, lithology principal name, lithology suffix,
  • principal lithology: breccia, igneous rock, mylonite, tephra, etc.
  • constituent: clasts (>2 mm), glass, groundmass, matrix, phenocrysts, etc.
  • fossil: bioturbation, calcareous nannofossils, fossil group, shell, etc.
  • formational structure: lamination, sedimentary structure, upper boundary or contact, etc.
  • deformational structure: fabric, fault, displacement, shear, etc.
  • orientation: CRF app. dip dir. 1 (90 or 270 deg), CRF app. dip angle 1 (deg), etc.
  • veins and vesicles: vein or veins, vein boundary, vein fill, vein shear, vesicles, etc.
  • alteration features: alteration patch, halo, static alteration, etc.


Micropaleontology templates use a few observables following the definition syntax for core description. The majority of observables are defined by the formal taxa definitions. The Template Manager application provides for several methods of converting taxa form entries or taxa lists into observables and adding them to templates.

Observable qualifier catalog

The observable qualifier catalog (or simply qualifier catalog) contains several hundred keywords that are used to create observable definitions. They are grouped into categories and subcategories.

Table observable qualifiers. 


Categories correspond to the GEODESC observable syntax elements (see Observable definition).

SubcategoryGEODESC designer grouping.
KeywordQualifier terms used to create an observable definition.
Changed onDate and time a qualifier was added.
Changed byAccount user name of person who added a qualifier.


An observation consists of the scope of description, the context given in the observable definition, and an observer entry that is compatible with the observable definition. 

Observer role

Observer is a formal role assigned to users authorized to use the Data Capture application.

Observer entry

Observer entry refers to the part of an observation that the observer enters in a cell. Observer entry is constrained by one of four validation types: text, list, numeric and formula. 


IODP uses 'piece' as a formal curatorial term. A piece is a part of a section (see scope of description), broken into its size and shape by the drilling process. Pieces may be a few cm to 10s of centimeters in length or consist of rubble. Pieces are numbered consecutively, starting at the top of each section. The top and the bottom offsets of pieces are defined by the positions of the plastic dividers that make up the bins constructed by shipboard personnel to contain the pieces.

Note: Core describers should not use pieces as the scope of description because a piece is a bad choice for defining a description interval. Description intervals should be based on visual characteristics (e.g., texture, composition) and may include parts of pieces or multiple pieces. The GEODESC scope of description has a feature column that automatically lists all the pieces included in a description interval.


A GEODESC project consists of a set of database tables that needs to be initiated for each new project. This is to ensure that each project can configure its templates to its specific needs, and given access to one or more expeditions samples as required and approved by program managers. All projects point to the GEODESC catalogs, which only exist in one instance as a shared resource. Also see Expeditions and projects.

Project templates

Project templates are copies of catalog templates modified using the Template Manager application to meet the project's needs. Project members wit the template maker role can also create new project templates from ground up. Project templates are defined as shown in Table <project template parameters>. Some of the parameters and their values are inherited from the catalog template that was copied to the project, others are only needed in the project.

Table <project template parameters>.

Database notationDatabase formatUser interface labelDescriptionFrom catalog
SCALEVARCHAR2 (50 BYTE)ScaleSee Template.YES

Large sample types

Small sample types

See Sample groups.YES
SAMPLE_TYPESVARCHAR2 (4000 BYTE)Sample typesSee Sample types.YES
HEADER_HEIGHTNUMBER (38)Header row heightDefault header row heigh for a template.YES
ROW_HEIGHTNUMBER (38)Data row heightDefault row heigh for all data rows in a template.YES
EXTENSIONVARCHAR2 (200 BYTE)Optional template name extensionAllows users to append additional information to the catalog project name for the benefit of the project team.NO
ALLOWED_EXPVARCHAR2 (4000 BYTE)Expeditions this template can useGEODESC administrator can specify the expeditions of which the samples can be described in a given project. Also see Expeditions and projects.NO


SECTION_FLAGVARCHAR2 (5 BYTE)When section length has changed, adjust 'bottom of sample' automaticallyIf checked (TRUE), user changes (corrections) to a section's length can be triggered to updated in the Data capture worksheet.NO
PERMISSIONVARCHAR2 (5 BYTE)Make template available to observersIf checked (TRUE), the template is available in the Data Capture application.NO
IGNORE_FLAGVARCHAR2 (5 BYTE)?? (For the CM we didn't implement?)NO
INVALID_FLAGVARCHAR2 (5 BYTE)?? (For the CM we didn't implement?)NO
PROJECTVARCHAR2 (50 BYTE)N/AThe project reference (typically a number) NO

Publish data

Users of the Data Capture application (observers) have a button on their data capture worksheets labeled Publish to LIMS. Data entered in the worksheet are autosaved, but not made available until users click the Publish to LIMS button, which triggers a data update in a different database table from where anyone can download data using the Data Access application. If the data are under moratorium, users need to sign in with the appropriate credentials.

Qualifier catalog

The GEODESC qualifier catalog contains geological terms that can be used to construct observable definitions. The terms are grouped into the 6 categories used in the the GEODESC observable definition syntax. Within each category, the terms are further grouped into topics that allow users to find related terms. 


Ranks are whole numbers that template makers can assign to values in entry validation lists.

  • Ranks associated with list values are convenient for plotting semi-quantitative data.
  • You can assign ranks to values in single-select validation lists.
  • Either all list items, or none, must be assigned ranks in any list.
  • Only whole numbers (integers and zero) can be used for the ranks.
  • The ranks appear in an automatically created column in the data capture worksheet.
  • A rank column will be automatically removed if the ranks are removed from the list values. 

Reviewer role

Reviewer is a formal role assigned to users authorized to use the Catalog Manager application. This role is intended for scientific staff members maintaining the GEODESC catalogs.


Sample is used as a generic term for any material recovered from a hole and processed and registered in the curatorial database. All samples in the JRSO LIMS are given a sample type designation. In GEODESC we furthermore group the sample types into large samples and small sample.

Sample types

All samples in the JRSO LIMS are given a sample type designation, which is primarily based on the way the samples were created (Table <sample types>). In GEODESC, the sample types are furthermore grouped into large and small sample groups

Table <sample types>.

Sample type codeSample type nameSample type description
Large samples

The cavity created with the drilling and coring action, and the walls surrounding that cavity.

CORECoreLong cylinders of material retrieved in a core barrel. A core may consist or fist to sand-sized fractured pieces as a result of the material properties and coring process..
SECTSectionArbitrarily (curatorial choice) cut segments of a core. The default length is 150 cm but many sections are curated at shorter lengths for a number of practical reasons. If the core is less than the length of a typical section it becomes a section.
SHLFSection half

Half-cylinder product of the along-axis split of a section, or its component fragments, through a selected diameter. Cross-sectional radius is nominally equal to that of the parent section.

The Data Capture application presents two 'sub-types' for convenience:

  • SHLF/A (section archive half) - core description is typically performed on the archive section half.
  • SHLF/W (section working half) - core description is only performed on the working section half if features cannot be observed in the archive section half.
WRNDWhole-roundCylindrical segments of core or core section material. They may be cut with the core liner for protection (e.g., sediment for physical properties studies) or they may be cut after splitting the liner and closer examination of the material (e.g., microbiological samples). The parent section length does not change when a WRND sample is taken. 
Small samples

A cylinder-shaped plug of material extracted from a parent sample. A cylinder is typically 5 - 20 cm3 in volume.

SSSmear slideA minute amount of material (a tooth pick sample) suspended in liquid and fixed on slide.
TPCKTooth pickMinute amount of material taken for observation, typically using a toothpick.
TSThin section

A sub-millimeter thick slice of material mounted on a glass slide.


A more or less regularly wedge-shaped sample extracted from a parent sample with a variety of tools. Wedges are typically 5-40 cm3 in volume.

WRNDWhole-roundCylindrical segments of core or core section material. They may be cut with the core liner for protection (e.g., sediment for physical properties studies) or they may be cut after splitting the liner and closer examination of the material (e.g., microbiological samples). The parent section length does not change when a WRND sample is taken. The whole-round sample is listed under small sample only because it is extracted as a parent sample from the core catcher (CC), assigned the test type PAL (paleontology), and is subsequently sub-samples for microfossil group-specific processing. The subsamples are tooth picks, wedges or whole-rounds and assigned test types such as NANNO, FORAM, DIAT, etc.
OTHROtherAny sample not fitting a specific category.

Sample groups

In GEODESC we group sample types into two groups, with specific implications. Large sample types are those where users define the description interval with top and bottom offsets with the section half, core and hole being the principal ones. Small sample types are those extracted from large sample types whereby the description interval was defined a the time the (sub or child) sample was created and the offsets cannot be changed in the GEODESC worksheet GEODESC.

Scope of description

The scope of description defines 'what' is being described. It consists of a sample identity (as registered in the curatorial database), a vertical (downhole) interval defined by the observer, an optional domain, computed depths for the interval, and a listing of pieces, if applicable. The full scope of description is represented by the first 18 columns in any data capture sheet. These columns can be hidden for the project template, but they can never be deleted and will appear in all final products data files for consistency.

Column headerDescription


These 7 sample identity parameters have been used in scientific ocean drilling for over half a century.

  • Exp is the expedition that recovered the cores from which the samples are to be described.
  • Site is the location at which coring/drilling is conducted. Sites are designated with a letter followed by a 4-digit number.
  • Hole is the specific hole at a site from which the samples were obtained. A letter suffix distinguishes each hole drilled at the same site. The first hole drilled is assigned 'A', the second hole 'B', and so forth.
  • Core is the largest sample type, up to ~10 m in length.
  • Type is a letter designating the coring system used to collect the core.
  • Section is a subsample of a core, typically cut to 1.5 m length for the convenience of handling and processing.
  • Section half is a designation for the two parts resulting from splitting a section along its axis. The designations A (archive half) and W (working half) are used to differentiate the type of processing and curation the material is subjected to.

These parameters are set and registered at the time the samples are created. When describing the material in GEODESC, observers select samples from a list of existing samples.


Section half

Sample IDThe concatenation of the above 7 parameters into a single dash separated string.
Offset top (cm)Offsets are measured from the top of sections and define the top and bottom of small sample types, or the description interval within large sample types. When small samples are taken from sections or section halves, the offsets are measured and recorded at that time. Therefore, when a template is configured for small sample types (usually for observations at the microscopic scale), observers cannot edit these fields. When describing large sample types (typically section halves), observers edit the offsets to define description intervals. This is the only case and place where observers can edit the content of scope columns.

Offset bottom (cm)
Top depth CSF-A (m)Core depth below seafloor, Method A (CSF-A) is the default depth computed according to IODP rules. The top and bottom depths correspond to the top and bottom of the description interval defined by sample curation and observer choices. The middle depth is computed for the convenience of having a single point for data presentation, which is particularly useful for small samples or structures.

Middle depth CSF-A (m)
Bottom depth CSF-A (m)
Top depth <alternate> (m)Alternate depths are computed according to IODP rules. The default alternate depth is the core depth below seafloor, Method B (CSF-B), where the the length of the recovered core is scaled to fit into the cored interval. If the project team constructs and uploads a core composite depth below seafloor (CCSF) scale to the JRSO LIMS database, that scale can be selected at the time the final product data files are downloaded from the database (using the Data Access application). The names of the alternate depth columns will be replaced with the CCSF scale name, and the alternate depths will be replaced with the corresponding depths.
Middle depth <alternate> (m)
Bottom depth <alternate> (m)
Domain no.

See Domains.

Piece no.If pieces are curated for a description interval, the piece numbers that overlap with the description interval are listed as a comma-delimited string in the Piece no. column.

Section lengths adjusted automatically

After a section length has been registered, the length may change by a small amount due to elastic and/or gas expansion (soft sediment cores), or as a result of complex curation procedures (igneous rocks). Core describers benefit from these changes being reflected automatically in the data capture worksheets, without having to check and fix discrepancies. Example: The a section length was registered as 150 cm, and a core describer has described the interval from 140 cm to the bottom of the section (BoS) as silty clay. The operator of the section half image logger (SHIL) later determines that the section half has expanded to 154 cm. A staff member updates the sample registry to ensure that the image is not inappropriately cropped. The automatic section length adjustment now ensures that the silty clay interval is automatically extended to the new BoS of 154 cm.

The automatic section length adjustment is enabled by default and can be disabled in the Template Manager application. In the Data Capture application, the Offset bottom is represented with the variable BoS (bottom of section). The BoS variable is converted to the actual Offset bottom (cm) registered at the time when the final product data file is generated.

Taxonomic catalogs

Taxa catalog

Taxa parameters

The Taxa catalog includes formally defined taxa vetted by specialists in the various microfossil groups. The taxa catalog also includes some informal taxa with appropriate reference information for those taxa that have not been formally named but are commonly used as biostratigraphic or paleoceanographic indicators. In addition, informal groups that are commonly identified during microfossil analysis are also included (e.g., fungal spores).

The GEODESC taxa table has 15 parameters described in Table <taxa parameters>. Parameters 2 through 12 are concatenated into the full taxon name. 

The entire catalog, or filtered parts of it, can be downloaded for a selected microfossil group using the Data Access application as tab-delimited text (*.txt) files.

Table <taxa parameters>. Parameters of the taxa catalog table and the validation rules used in the Catalog Manager (CM) and Template Manager (TM) applications.

Col.GEODESC Column headerGlobal taxa validation ruleEntry controlCM entry basic requirementCM entry duplicate checkTM check 1TM check 2
1Microfossil groupMust be one of the standard GEODESC groups. Must be spelled lower case.Dropdown listRequired

2Order/Family/Informal Group (OFIG)This column or the Genus column must have an entry.NoneConditionally requiredYESYESYES



This column or the OFIG column must have an entry. First letter must be upper case.NoneConditionally requiredYESYESYES
4Species modifierIf a Species modifier exists, it must be a value from the allowed list of values.Dropdown listOptional
5SpeciesIf a Species exists, a Genus must be present. First letter must be lower case.NoneOptionalYESYESYES
6Subspecies modifierIf a Subspecies modifier exists, it must be a value from the allowed list of values.Dropdown listOptional
7SubspeciesIf a Subspecies exists, a Species and Genus must be present.NoneOptionalYESYESYES


Size (numeric) If a Size (numeric) exists, it must be in the allowed format: size must be a number, unit must be microns or mm.Numbers and unitsOptional
9SuffixIf a Suffix exists, it must be a value from the allowed list of values.Dropdown listOptional
10Descriptive textNone.NoneOptional
11Sensu (reference)The reference follows the standard rules for parentheses, etc.. Names are capitalized according to the standard orthographic rules.NoneOptionalYESYESYES
12ReferenceThe reference follows the standard rules for parentheses, etc.. Names are capitalized according to the standard orthographic rules.NoneRecommended
Additional information (entered in catalog if available, for the purpose of filtering/selecting taxa, but not captured in project.
13AgeFollows stratigraphic capitalization rules.NoneOptional

14Marker taxon

15Geographic distribution

Summary of taxa validation rules

  1. The combination of the following taxa parameters is used to check for the existence of a taxon in the catalog, ignoring potential modifiers:
    1. Microfossil group
    2. Order/Family/Informal group
    3. Genus
    4. Species
    5. Subspecies
    6. Sensu (reference)
  2. Additional rules:
    1. Microfossil group is required because it is used for filtering purposes in the GEODESC apps. The value must be selected from the GEODESC list of microfossil groups.
    2. A taxon must include either an Order/Family/informal group or a Genus (not both). This is the minimum definition of a taxon, i.e., no other information is required.
    3. Genus must be capitalized.
    4. If a Species is entered, a Genus is required.
    5. An entry in Subspecies requires an entry in both Genus and Species.
    6. Species and subspecies must be all lower case.
  3. The modifying parameters are for use in project templates (added using the Template Manager app) and should in general not be used in the catalog:
    1. Species modifier
    2. Subspecies modifier
    3. Size (numeric)
    4. Suffix
    5. Descriptive text
  4. Additional rules:
    1. Modifiers are technically allowed in the catalog for the rare cases where specialists feel that certain modified taxa should be in the catalog.
    2. Modifiers must be selected from the GEODESC modifier lists.
    3. Size (numeric) must conform with the following formats, operators and units (numbers can have decimals and are just for illustration here):
      1. > 3 microns
      2. =3 microns
      3. <10 mm
      4. =10 mm
      5. 5-10 microns
      6. 1-2 mm
    4. Descriptive text is a free form entry that can be used to add information that is not available via the modifiers. It is more typically used in a project template rather than the catalog.
  5. The parameter Reference should be provided in a catalog entry. We currently have no validations. Different format preferences exist among micropaleontologists, e.g., for "&" vs. "and". Project templates don't need this parameter.
  6. The three additional taxon information parameters may be provided in a catalog entry. They can also be added separately after the taxa have been imported.
    1. Age
    2. Marker taxon
    3. Geographic distribution

Synonym catalog

The GEODESC Synonyms catalog consists of synonyms of taxa in the Taxonomic catalog. The synonyms table has has the same first 12 parameters described in Table <taxa parameters>. It does not have parameters 13-15. The synonym catalog has one additional parameter:

Allow flag

Each synonym is designated as either "allowed" (ALLOW_FLAG = TRUE), i.e., it can be used in a GEODESC template, or "denied" (ALLOW_FLAG = FALSE), i.e., cannot be used in a GEODESC template. Synonyms that are not allowed include invalid taxa, former names that are no longer used, misspellings, etc. Allowed synonyms are typically taxa where different paleontologists apply different names for the same taxonomic concept. A common example is when a taxon is transferred to a different genus but many paleontologists still use the previous genus name. The Synonym catalog is not exhaustive and is updated as directed by expert users.


A GEODESC template is a collection of observables for a description topic. Templates exist in two implementations: catalog templates and project templates.

  • Catalog templates are carefully crafted collections of observables based on a decade worth of data from past expeditions. Catalog templates exist for typical lithotypes, microfossil groups, and other description topics. Template makers select those most suitable and copy them to the project. See the observable catalog section for information on observables and their attributes.
  • Once copied to a project, catalog templates can be used 'out of the box', or modified in any way based on project team consensus, using the Template Manager application.
  • Project templates implement observables as spreadsheet columns for data capture.

Both catalog templates and project templates each have three defining key attributes, which make up the unique template name and can be used in searches:

  • Scale: Three fixed scales for description:
    • microscopic
    • macroscopic
    • summary (for summarizing macroscopic and microscopic observations for sections, cores and holes.)
  • Type: A list of fixed, geologically intuitive values to choose from (used for filtering in other tables):
    • sediment
    • igneous
    • structures
    • microfossils
    • general
  • Objective: The unique description of what kind of observations the template is designed for.

Project templates have two additional parameters for practical purposes:

  • Extension - A way for the template maker to communicate updates to the observers. The extension can be edited elsewhere and will be part of the final data file name.
  • Permission - A flag the template maker can set elsewhere. It determines whether the observers can use the template for data capture or not.  

Template catalog

The template catalog is an inventory of all data capture templates designed based on past IODP usage and available for immediate use. Once catalog templates are copied to a project using the Template Manager application, they can be modified to the project members' needs. Parts or all of the catalog can be downloaded at any time in the form of tab-delimited text (*.txt) metadata files, using the Data Access application

Template maker role

Template maker is the formal role designation of a user who has the credentials to use the Template Manager application.

Template makers can:

  • copy existing catalog templates to the project;
  • modify project templates to suit the needs of the projects;
    • modifications made to a project template do not affect the original catalog template, the modifications made to that template in other projects, or any other project template.
  • create new templates;
  • add observable columns to the template and set their attributes, including validation criteria. 

The template definitions are stored in an Oracle database and users can download tab-delimited metadata files describing the templates, using the Data Access application.

Template Manager application

The GEODESC Template Manager (TM) application is used to prepare the project templates a project team is using to collect descriptive data. It is a web app that can be used on any browser if the GEODESC administrator has created the project, provided a user account, and configured the account with the application (template maker) and project credentials. The TM app allows template makers to:

  • copy existing catalog templates to the project, turning the copies into project templates;
  • modify project templates to suit the needs of the projects, whereby modifications made to a project template do not affect the original catalog template, the modifications made to that template in other projects, or any other project template. 
  • create new project templates if a suitable catalog template to start out with doesn't exist; 
  • add observable columns from the catalog, or create new ones in the project, whereby micropaleontologists can create batches of columns based on taxa lists;
  • edit column attributes, including data entry validation criteria and display formats. 

The template definitions are stored in the GEODESC database and users can download the definitions in tab-delimited metadata files using the Data Access application.

Go to the Template Manager application user guide.

Test types

At the time of sample creation, a test type can be assigned to the sample in addition to the mandatory sample type. Whereas sample type is based on how the sample was created, or its physical shape, test type is assigned based on the planned analytical objective for the sample. The Data Capture application shows all existing test types for the selected sample types and users can filter the samples to be added to the worksheet by selecting the desired test types.

  • Large sample types have traditionally not had a test type assigned.
  • Small sample types have a number of possible test types, which are assigned by the technician or scientist who creates and/or registers the sample. The test types typically useful for microscopic description in GEODESC are:
    • DIAT
    • FORAM
    • NANO
    • PAL
    • RAD
    • SS
    • TS

Whole-round sample scopes created automatically

When core describers receive the section halves for description, intervals may be missing where whole-round samples (sample type WRND) were removed early in the core handling process. The gaps created in the section (halves) are typically filled with styrofoam marked as 'WRND', however, if the sample was taken at the bottom of a section, a yellow end cap indicates that this happened but the WRND sample length is not known without consulting the sample report. Examples: WRND samples were removed for physical properties or microbiological experiments and may have been briefly described from their surface appearance, but typically are not; or WRND samples were removed to squeeze interstitial water and in that case were typically not described.

GEODESC has a feature whereby the WRND sample scopes are automatically created and inserted as separated rows when the observer adds a section or section half to the worksheet. This ensures that the WRND sample scope, which has the same sample ID as the parent section, has the exact offsets recored in the sample registry, without the observer having to look them up in a sample report table. All the observer has to do is select 'WRND' from the list in the 'No material present' observable column. 

This feature is enabled by default in the Template Manager application and can be disabled if needed by un-checking the relevant check box. 


A workset is defined in the Data Capture application by a template, a hole, and optionally a set of cores that an observer wants to describe. Based on the user-defined workset, the application creates a worksheet (or multiple worksheets in a workbook). The purpose of defining worksets is to protect an observer’s data entry from interference by another user - only one user can edit a workset at a time. When a work set is 'checked out', it is flagged as 'in use' and only the current user can capture data for that workset. A user can release a workset and make it available to another user.


A workbook is a collection of worksheets created by the Data Capture application based on workset definitions. Observers capture observations in the workbook and save them to the database. 

Worksheet columns

Worksheet columns are the observable instantiations in a project template.

Table <worksheet column parameters>.

Database notationDatabase formatUser interface labelDescriptionFrom catalog
HEADERVARCHAR2 (200 BYTE)HeaderThe column header assigned in the catalog template or by users in the Template Manager application.





SORTORDERNUMBER (4)SortorderThe order the columns appear in the worksheet.YES
IGNORE_FLAGVARCHAR2 (5 BYTE)?? (For the CM we didn't implement?)NO
INVALID_FLAGVARCHAR2 (5 BYTE)?? (For the CM we didn't implement?)NO
COMMENTSVARCHAR2 (1000 BYTE)Optional commentAn informal comment a template maker can add to a newly created column.NO

Zone catalog

The zone catalog lists all zones for all relevant, published biostratigraphic zonal schemes so micropaleontological observations can be associated with zones. Template makers can select a zonal framework publication reference and add a column to the template using the Template Manager application. Next, template makers can select the range of zones applicable to the project samples and those zones will be available from a dropdown list in the Data Capture application. 

Zone catalog table 1. The zone catalog has six parameters presented as columns.

ParameterParameter description
Sort orderA single number series for all zones of all zonal schemes in the GEODESC catalog.
Zone code
Zone name
Zone reference
Microfossil group


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