J-CORES, D/V Chikyu Science Data Management System

Overview

J-CORES is a scientific data management system in order to collect and store science data taken on D/V CHIKYU shipboard.

The data stored by the system are being distributed by SIO7 Data Center and http://kcc-iodp-data.jamstec.go.jp.

Components

Version 1.9 is the latest stable one.

diagram of J-CORES' components

The system consists of a database and some client application softwares. They are typically deployed on a host computer and some different computers, respectively. The applications are divided by their use cases.

CompositeLogViewer

Application ‘CompositeLogViewer’ visualizes multiple data in depth series immediately after data entry to the database by the other applications: They include VCD, numerical values measured instrumentally and core recovery in any processed depths. [User's manual]

Bulk Export CLI

‘Bulk Export’ function exports all the data on the database. The equal function can be executed by using CompositeLogViewer. [User's manual]

D-Tunes

Application ‘D-Tunes’ processes depths. Any number of processed depths can be recorded either from measured depths of core depth (the way to indicate horizons in cores, i.e. site/hole/core/section/interval), drill pipe depth, wireline logging depth, mud logging depth and seismic TWT, or from other processed depths. [Presentation slide] [User's manual]

Visual Core Description (VCD)

Application ‘VCD’ is for shipboard sedimentologists, petrologists and structure geologists to perform visual core description (VCD). [Screen shooting movies 1 2 3 4] [Practical instruction of live VCD during CK06-06 cruise, in Japanese] [User's manual]

Uploader

Application ‘Uploader’ is to read data files in a specific format and load them onto the database. [User's manual]

Operation

Application ‘Operation’ is to add and edit sites, holes and core drillings. [User's manual]

Curation

Curators record core sections, miscellaneous materials (physical materials recovered from a hole, excluding cores, e.g. mud logging cuttings, side wall micro-cores by a wireline logging tool, in-situ water samples by a downhole tool), sample requests and sample codes by using Application ‘Curation’. [User's manual]

Sample

Each sample is taken from a core section or a miscellaneous material and is recorded by Application ‘Sample’. [User's manual]

User

Application ‘User’ is for user administration. [User's manual]

Parameter Definer

‘Parameter Definer’ is a command-line interface to define ‘User-Defined Parameter’ and to look the definition. [User's manual]

Database Synchronizer

‘Database Synchronizer’ is for merging and splitting data between two databases. [User's manual]

Data Model

The entity relationship diagrams (ERD) and the list of table columns present the data model. [ERD; ERwin, pdf: Column list; pdf]

History

Development of the system was initiated in 2000. The first version 0.1 (2002-02) contained Application ‘CompositeLogViewer’ which connected to Janus clone database. From Version 0.2 (2003-02), it was started to develop Applications ‘VCD’, ‘Uploader’ and ‘Stratigraphy’ with data model contains many original tables additionally. In Version 0.3 (2004-01), ‘VCD’ had capability to describe sedimentary, hard rock, and deformation structures, and gradated or alternated lithology. ‘Uploader’ could load files of magnetometries.

Version 0.4 (2005-04) contained Applications ‘Operation’, ‘Curation’, ‘Sample’ and ‘User’. The data model became that of J-CORES. ‘Stratigraphy’ was capable to develop references of chrono-, magneto-, bio-, and lithostratigraphic unit and horizon, and bibliography. Uploader could load files of geochemical measurements. Version 0.5 (2005-08) included Application ‘D-Tunes’, and the capability of ‘Uploader’ to load extra data in CSV files. Data model of stratigraphic horizon recognition and age model was also built as well as file format specifications. Application ‘µBio’ was included by version 0.6 (2005-10-03). Version 0.7 (2005-10-31) had the capability to store XRD measurement. ‘CompositeLogViewer’ of Version 0.9 (2006-07-28) had diagram template function and SVG export function. Versions 0.8 (2006-07-26), 0.10 (2006-08-01), 0.11 (2006-08-12) and 0.12 (2006-09-19) were unstable versions whose ‘CompositeLogViewer’ are fast. Version 1.0 (2006-11-28) had the diagram template and SVG export functions of Version 0.9 and its ‘CompositeLogViewer’ and ‘VCD’ were as fast as Version 0.12.

Version 1.1 (2007-08-31) included the function of ‘Bulk Export’, which exported all the data shown by ‘CompositeLogViewer’ into a CSV file and some attaching files. The function was in order to provide data to IODP SMCS and SEDIS. In order to co-work with IODP SMCS, Version 1.2 (2007-11-13) was capable to store SMCS' approved sample request ID list, upon which samples were taken. Version 1.3 (2008-03-31) included Administration Tools ‘Database Synchronizer’ to divide and migrate data between the ship and land databases. Versions 1.4 and 1.5 (2009-04-30) had the following enhancements: 1. Saving the previous view setting in Applications CompositeLogViewer and VCD; 2. Improved VCD human interface and drawing function; 3. Handling measurements outside curated length of core sections by CompositeLogViewer; 4. Visualization of most of parameters of the moisture and density and anisotropy of magnetic susceptibility by CompositeLogViewer; 5. Lock and unlock function for section and miscellaneous material halves from sampling from them. Version 1.6 (2010-05-10) renamed built-in measured and processed depths and their units in accordance with ‘IODP Depth Scale Terminology’ Version 1.1. Version 1.7 (2011-06-30) was an unstable version in order to test the application programs on Java SE 6. By Version 1.8 (2012-05-07) the function to load ‘Extra Scalar’ values in ‘CSV File’ was replaced by a new capability to store ‘User-Defined Parameter’, which accepts numerical values, text values and attachment files for expedition, seismic shot points, sites, holes, cores, miscellaneous materials, sections, samples, horizons and intervals. Application ‘Visual Core Description’ enables to copy & paste lithology-distributions, their boundaries, structures and drilling disturbances within the application. Applications of Version 1.9 (2013-08-30) ran on Java SE 7. The following applications and functions went out of support: Application ‘Stratigraphy’, Application ‘µBio’, components ‘graphic representation editor’, ‘VCD slide editor’ and ‘summarized-lithounit editor’ of Application ‘Visual Core Description’ and functions of Application ‘Uploader’ to load all the kinds of data, excepting data for ‘User-Defined Parameter’.

Ownership

Center for Deep Earth Exploration (CDEX), Japan Agency for Marine-Earth Science and Technology (JAMSTEC) owns the set of the software programs. Currently, they are not distributing the software.