LORE for SCORS

1. Introduction

LORE stands for LIMS (Laboratory Information Management System) Online Reports, LORE is the main portal for users on the JOIDES Resolution (JR) and on shore to access data generated on the JR or in the Gulf Coast Repository (GCR).

LORE is used in two ways in the stratigraphic correlation workflow:

  • Download image data for correlation

    • Most data used in the Correlator app are more conveniently downloaded from LIMS using the Correlation Downloader app because it provides special features and formats used in that workflow. One exception are images, which at this time are not integrated in the Correlation Downloader.

  • Access the affine and splice data generated in Correlator and uploaded to the LIMS.

    • List of affine tables

    • Affine tables

    • List of splice interval tables

    • Splice interval tables

  • Access any data in LIMS with the CCSF depth appended.

  • Access data in LIMS by splice.

2. Download image data for correlation

  • Go to the LORE page at

  • Select the Images > Core Section (LSIMG) > Standard report

  • Select the hole for which you want to reduce the section half images

  • Click View data, then click Batch download linked files

  • When prompted, click Cropped image (JPG link)

  • Click the Chose a link button.

    • A zip file with all the images will be written to whatever download folder your workstation has configured.

3. Access affine and splice data

3.1. List of affine tables report

This report lists the CCSF alternate depth scales available in LIMS, and the original affine table files that the scales are derived from, one per row (Fig. 5-2). Metadata for each scale are provided as well (see Table 6 for column descriptions). The list can be filtered by entering an expedition number.

To get a list of affine tables report (Fig. 5-2):

  • In the Select report panel, expand the Stratigraphic Correlation list and select List of affine tables report.

  • In the Hierarchy Search area, filter by Expedition(s), if so desired.

  • View data on screen using the View data button.

  • Option: download data in CSV format using the Download tabular data button.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 1: List of affine tables report.

 

 

Table 1. Description of List of affine tables report columns.

Column name

Description

Alternate depth scale (CCSF) name

This formal name is auto-generated at the time of upload, based on the contents of the affine table file uploaded by the user and an optional, up to 10 character long extension at the end (after the date) directly entered by the user.

Uploaded affine table file name and link

The file name is exactly the same as that of the original, unaltered user file, which can be downloaded via the link.

Date and time of upload

Date and time based on database server settings.

User comment

User who uploaded the affine table file may have entered an optional comment at the time of file upload, to communicate pertinent process or file information to future users of the data.

Name of account used to upload

Name of the LIMS user account that was used to upload the affine table file.

 

3.2. Affine tables report

This report provides the full affine table information, one core per row (Fig. 5-3; see Table 5-2 for descriptions of columns). Sample identity information (i.e., hole and core) and the cumulative offset for each core resulting from depth shifting, are derived directly from user-uploaded files. However, the CSF-A and CCSF depths as well as differential offset and growth rate are computed in LIMS, based on latest sample registry data for hole and core. The original, unaltered affine table user file can also be downloaded.

To get an affine table report (Fig. 5-3):

  • In the Select report panel, expand Stratigraphic Correlation list and select Affine Tables report.

  • In the Additional Filters area, use the Alternate depth scale choice list to select the scale corresponding to the appropriate affine.

    • You can reduce the choice list by selecting an expedition from the Expedition(s) filter in the Hierarchy Search area.

  • View data on screen using the View data button.

  • Option: download data in CSV format using the Download tabular data button.

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 2: Affine table report.

 

Table 2. Description of Affine tables report columns.

Column name

Description

Site, Hole, Core, Type

Sample identity of the core.

Depth CSF-A (m)

Top of core depth from the LIMS sample registry at the original CSF-A depth scale.

Depth CCSF (m)

Top of core depth at the CCSF alternate depth scale.

Depth CCSF (m) = Depth CSF-A (m) + Cumulative offset (m)

Cumulative offset (m)

Distance a core was shifted along the depth axis relative to the original CSF-A depth.

Differential offset (m)

Distance a core was shifted along the depth axis relative to its depth after the next shallower core was shifted. This value, when viewed in context, is useful to detect unusual shifts that may indicate a correlation error or stratigraphic irregularity.

Growth rate

Growth rate = Depth CCSF (m) / Depth CSF-A (m); a measure of the degree of expansion in the recovered sediment section relative to the in-situ section.

Shift type (optional comment)

Recommended terms are: anchor, tie, set, and append. See section 2 of this user guide for explanation.

Data type used (optional comment)

Recommended terms are analysis names or acronyms, such as NGR, MSL, RGB, etc.

Quality comment (optional comment)

Recommended comments are those pointing to problematic shifts based on less than ideal signal.

 

3.3. List of splice interval tables report

This report lists the splice interval tables available in LIMS, one per row, including metadata and links generated by the LIMS or added by the user at the time of file upload (Fig. 5-4; see Table 5-3 for description of columns). The list can be filtered by entering an expedition number.

To get a list of splice interval tables report (Fig. 5-4):

  • In the Select report panel, expand Stratigraphic Correlation list and select List of Splice Interval Tables report.

  • In the Hierarchy Search area, filter by Expedition(s), if so desired.

  • View data on screen using the View data button.

  • Option: download data in CSV format using the Download tabular data button.

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 3: List of splice interval tables report.

 

 

Table 3. Description of List of splice interval tables report columns.

Column name

Description

Splice name

This formal name is auto-generated at the time of upload, based on the contents of the splice interval table file uploaded by the user and an optional, up to 10 character long extension at the end (after the date) directly entered by the user.

Associated CCSF scale (affine table)

CCSF alternate depth scale (based on affine table), selected by the user who uploaded the splice interval table.

Uploaded splice interval table file name and link

The file name is exactly the same as that of the original, unaltered user file, which can be downloaded via the link.

Uploaded splice tie point table file name and link

Upload of this type of file is optional. File name, if present, is exactly what users named it; link downloads the unaltered file.

Date and time of upload

Data and time based on database server settings.

User comment

User who uploaded the splice interval table file may have entered an optional comment at the time of file upload, to communicate pertinent process or file information to future users of the data.

Name of account used to upload

Name of the LIMS user account that was used to upload the affine table file.

 

3.4. Splice interval tables report

This report provides the full splice interval table information, one interval per row (Fig. 5-5; see Table 5-4 for descriptions of columns). Sample identity information (i.e., hole, core, section, offset) is derived directly from user-uploaded files. However, the CSF-A and CCSF depths are computed in LIMS, based on latest sample registry data for hole and core. The original, unaltered splice interval table user file can also be downloaded.

To get an affine table report (Fig. 5-5):

  • In the Select report panel, expand Stratigraphic Correlation list and select Splice table report.

  • In the Splice Search area, use the choice list to select the appropriate splice.

    • You can reduce the choice list by selecting an expedition from the Expedition(s) filter in the Hierarchy Search area.

  • View data on screen using the View data button.

  • Option: download data in CSV format using the Download tabular data button.

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 4: Splice table report.

 

Table 4. Description of Splice interval tables report columns.

Column name

Description

Interval

Sequential numbering of splices intervals added by LIMS.

Site, Hole, Core, Type

Sample identity of the core.

Top section

Section number of top and bottom of splice interval, respectively.

Top offset (cm)

Offset of top of splice interval.

Top depth CSF-A (m)

CSF-A depth of top of splice interval.

Top depth CCSF (m)

CCSF depth of top of splice interval.

Bottom section

Section number of bottom of splice interval.

Bottom offset (cm)

Offset of bottom of splice interval.

Bottom depth CSF-A (m)

CSF-A depth of bottom of splice interval.

Bottom depth CCSF (m)

CCSF depth of bottom of splice interval.

Splice type (optional comment)

Recommended terms are given in Table 4 (Section 2).

Data type used (optional comment)

Recommended terms are analysis names or acronyms, such as NGR, MSL, RGB, etc.

Quality comment (optional comment)

Recommended comments are those pointing to problematic intervals based on less than ideal signal.

 

4. Access LIMS data with alternate depths

This report feature provides CCSF alternate depth for any sample and data point in any data report that uses depth (CSF-A) as the primary independent variable. User must select the appropriate alternate scale for a report.

To retrieve CCSF depths with data (Fig. 5-6):

  • In the Select report area, select desired data type by expanding the category of interest.

  • In the Hierarchy Search area, filter Expedition(s), Site(s), Hole(s), Core(s), etc., as needed.

  • In the Additional Filters area, select the appropriate Alternate depth scale from the choice list.

  • View data on screen using the View data button. The alternate depths will be shown in the column nest to the CSF-A depths.

  • Option: download data in CSV format using the Download tabular data button.

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Figure 5. Data report example with alternate depths shown in column #10.

5. Data by splice

One of the major goals of stratigraphic correlation is to generate “spliced data”, or to retrieve “data by splice”. To get data by splice (Fig. 5-7):

  • In the Select report area, select desired data type by expanding the category of interest.

  • In the Splice Search area, select the appropriate splice from choice list.

  • You can filter the splice list by selecting an expedition in the Hierarchy Search area.

  • View data on screen using the View data button. The alternate depths will be shown in the column nest to the CSF-A depths.

  • Option: download data in CSV format using the Download tabular data button.

 

 

 

 

 

 

 

 

 

 

 

 

Figure 6. Data set extracted for user-selected splice.

 

 

Appendix 1: Specifications for affine tables

The affine table exported from Correlator has the 15 columns described in the table below. In order to take advantage of the features offered from within the LIMS database, affine tables exported from Correlator or any other correlation programs must meet import requirements of the SCORS Uploader and Manager application. As a minimum requirement, the first 7 columns must be present.

 

Affine table column headers

Format

Examples values

LIMS upload file requirements

Upload validation

LIMS report sourcing

Site

text

69, 1103, U1423

Presence of columns required

Validated against identities in LIMS

From upload file

Hole

A, B, C, .....

Core

integer

3, 45, 138

Core type

text

H, X, R, ....

Not validated

From LIMS computations

Core top depth CSF-A (m)

number

2.3, 124.175, 1504.4

Core top depth CCSF (m)

Cumulative offset (m)

-0.560, 4.562, 48.392

Number format validated

From upload file

Differential offset (m)

Presence of columns optional

Not validated

Growth rate

0.91, 1.05, 1.21

Shift type

text

REL, TIE, SET

Data used

NGR

Quality comment

“Interval includes core disturbance”

Reference core

A3, B15, C123

Not reported from LIMS

Reference tie point CSF-A (m)

number

2.3, 124.175, 1504.4

Shift tie point CSF-A (m)

 

 

 

Appendix 2: Specifications for splice interval tables

 

The splice table exported from Correlator has the 15 columns described in the table below. In order to take advantage of the features offered from within the LIMS database, splice tables exported from Correlator or any other correlation programs must meet import requirements of the SCORS Uploader and Manager application.

 

Current header in Correlator 2 and 3

Format

Examples

LIMS upload file requirements

LIMS upload validation

LIMS report sourcing

Site

text

69, 987, 1103, U1423

Presence of all columns is required

Validated against identities in LIMS

From upload file

Hole

A, B, C, .....

Core

integer

3, 45, 138

Core Type

text

H, X, R, ....

Top Section

1, 12, CC

Top Offset

number

1.2, 45, 151.7

Top Depth CSF-A

2.3, 124.175, 1504.4

Not validated

From LIMS computations

Top Depth CCSF-A

Bottom Section

text

1, 12, CC

Validated against identities in LIMS

From upload file

Bottom Offset

number

1.2, 45, 151.7

Bottom Depth CSF-A

2.3, 124.175, 1504.4

Not validated

From LIMS computations

Bottom Depth CCSF-A

Splice Type

text

TIE, APPEND

From upload file

Data Used

NGR

Comment

“Might include slumped bed”