Overview

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). 

The GEODESC system includes five browser-based user applications backed by an Oracle database (Figure 1):

• The Data Capture application is based on the widely used and user-approved method of capturing observational data in spreadsheets: A row represents a description interval, and the columns specify the scope of the observations and the observables. You need the  observer role assigned to your database account to use the app for your project. 
• The Template Manager application allows you to make any changes you need to your project templates. You need the template maker role assigned to your database account to use the app for your project project.
• The Data Access application allows anyone to download the final description files and template metadata files, on the ship and on shore. Access to data is moratorium protected.
• The Catalog Manager is a tool to gradually update the GEODESC catalogs used in the Template Manager app into the future, based on actual use. Only qualified support people are given the reviewer role to update the catalog.
• The Taxa File Checker application facilitates the creation of micropaleontology templates using validated taxonomic name lists. Anyone can use this application.

Figure 1. GEODESC overview diagram.

Data Capture application

Observers using DC select one or more project templates they are qualified for, select the hole (and optionally a subset of cores) they 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.

Observers enter data into the worksheets 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 for data safety, however, to make the data available to non-GEODESC users, observers tap the 'Upload button', which creates an updated final product file. An upload initiates a sort and a validation and flags all errors that are not already flagged. Data cannot be uploaded unless all errors are fixed.

The first set of 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 observable 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 providing template configuration information.

The Template Manager application

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 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 placed on setting entry validations. Decades of practical experience in the intense 24/7 collaborative and technician-supported data gathering operations on the JR taught 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 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 a few to several days into the project, with minor changes later on.

The Data Access application

A dedicated data access page allows any user to search for and access any final product files. This is true anytime for project team members, and it applies to the world once the data are out of moratorium. 

The Catalog Manager application

The GEODESC catalogs feature all that core describers and paleontologists need - to the best of our current knowledge. However, not only are we not perfect, we also know that project requirements evolve and if the tools set is to serve the community for many years, expert users must be able to update the catalogs. the CM therefore allows credentialed staff members to update any part of the catalog using a 'review project'. Reviewers can directly create a template with the new features in TM, using the review project, and then load it to the catalog for future availability in TM. The review project can also be loaded with an expedition project and the reviewer can load selected items to the catalog.

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.