Purpose and concepts

The GEODESC application tool set was designed and built in 2019-2022 to support geological core description and micropaleontological data capture on the scientific drilling vessel JOIDES Resolution (JR). 

GEODESC is based on the widely used and user-approved method of capturing observational data in spreadsheets. A row represents a description interval or domain, with any number of observations as required by the project. The first set of 13 fixed columns defines 18 columns in each worksheet define the scope of description (sample identity, sample interval, computed depth, etc.), and these are followed by any number of user-configurable columns define observables, where each observable can have its own validation rulesobservable columns. A project uses multiple spreadsheet templates based on the scale, type and objective of observations. The final data products consist of tab-delimited text files, one data file per template and hole, and one metadata file per template with providing template configuration information.

GEODESC allows observers to use existing templates from a catalog, and to modify catalog templates or create completely new ones. The catalog templates were configured based on the experience gathered during decades of scientific ocean drilling with hundreds of expeditions.   The GEODESC system includes five browser-based user applications backed by an Oracle database (Figure 1). The two main user applications are the Template Manager application (TM) and the Data Capture application (DC), and users must be credentialed as template makers and observers, respectively, to use them for a specific project. All qualified core describers and paleontologists are observershave the observer role, but not all observers need to be template makers. The Data Access application is publicly available through the Laboratory Information Management System (LIMS) and allows all project team members to download final product files on ship and shore, and the public can do so after the data moratorium has expired. The Catalog Manager is a tool to update the GEODESC catalogs used in TM and only qualified support people are given this role. Finally, a small helper application, the Taxa File Checker, facilitates the creation of taxonomic name lists for use in GEODESC, and validates them against the taxa catalog.

Templates rule

All template modifications that affect the final product data files are made using TM. Template makers rely heavily on the availability of catalogs to select and configure their project templates. This begins with the selection of a suitable subset of catalog templates, which were configured based on the experience gathered during decades of scientific ocean drilling with hundreds of expeditions. If a catalog template is mostly but not exactly suitable for the project, template makers can modify them and even create completely new templates. TM includes features to search and add catalog observable columns or columns from the observable catalog, create new observable columns using specific methods for core material descriptions and micropaleontology, delete and reorder columns, set entry validations for observable columns, and set some basic formats.

Emphasis is The unique emphasis placed on setting entry validations in TM stems from decades . Decades of practical experience in the intense 24/7 , collaborative and technician-supported data gathering operations on the JR . We learned that allowing on-the-fly template modifications by each observer in DC adversely affects the data producttaught us that the expected scientific data consistency and integrity requires rigorous entry validation. Entry validation features include basic concepts such as single-select and multi-select value lists and numeric controls to ensure team consensus on choice lists as well as consistent data collection by avoiding and avoid accidental spelling errors and erroneous numbers. Other entry validation features are more specific to the geological application, such as stratigraphic contiguity, and making appropriate use of the rich sample registry available to GEODESC users. The template making process typically concludes early in a few to several days into the project, with possible minor changes later on.

Efficient data capture

Observers using DC select one or more project templates for a they are qualified for, select the hole (and optionally a subset of cores) to create worksets, which are the instantiated as workbooks that only one observer can use for data entry. Observers must release worksets for others to be able to create worksets using the same templates and coresthey are observing for their work sessions, and so define and 'check out' worksets that other observers cannot use until they are released. Worksets are then instantiated as workbooks in a browser. All observers can check the workset dashboard at any time to see who is working on what.

Once in a selected worksheet, observers enter data as they would in any modern spreadsheet program, except that they are supported and constrained by many special features designed to make data capture efficient and to ensure data integrity to the degree possible given the level of observational expertise in the project team. The initial worksheet is empty and observers must selected available samples using a sample selector feature with versatile filters applied to the LIMS sample registry. Each sample added to the worksheet adds a row, representing the scope of description. Some scopes can be further divided into sample intervals and domains using special row context menus. Data entries are immediately autosaved to the database, 

Figure 1: Schematic overview of GEODESC users, user applications, and database 'backbone'.

Limitations for external use

The GEODESC tool set is taking advantage of existing tools and resources on the JR for efficient data gathering and reporting, and therefore cannot easily be used outside the JR computing infrastructure. Most importantly, GEODESC is using

• the sophisticated sample registry that evolved over decades to accommodate user needs, and
• depth computation business rules for standard depths and alternate depths

If GEODESC was to be fully used in another organization, these resources would have to be replicated or replaced.

However, external projects can take advantage of the GEODESC catalog resources and final product data files, all available in tab-delimited text format, and use them in commercial spreadsheet programs with or without adding sample registry and data validation functions.