TRISH User Data Management Tool Instructions

Content-

• Basic Information

• How to open the tool

• Uploading tree-ring data

• Usage
• Metadata file format
• Tree-ring data file format
• Data copyright statement

• Managing tree-ring data

• Usage

Basic Information

The User Data Management Tool (UDMT)l allows a registered user to upload and manage his/her own tree-ring data to the TRISH-Web system and use it for single- and multi-site hydrological and climate reconstructions. Each upload action/push of the user data creates its own tree-ring database node with a unique identifier that is used by the system to display it in the pool of the available data as a site group listed in the data selection filter. The design of the tool interface is simple, intuitive, and can be easily learned by any interested scientist/user. The key feature of the UDMT is an option for the user to set access permission for the data as public or private and to change it anytime after the data is uploaded to the system.

How to open the tool

To open the tool, click the “Add/Update” button on the Data Filter bar just below the Web page title and above the interactive map area -

Clicking on the Tool opens a pop-up window -

The UDMT has two sections, based on the tool purpose -

1. Managing previously uploaded data which is highlighted by light green (mint) color, and
2. Uploading new user data which is highlighted by the peach background color.

Below we describe the main tool functions and how to use them.

Uploading tree-ring data

Usage

The UDMT allows a registered and logged on user to upload their own tree-ring dataset to the system for climate reconstruction.  Reconstruction can be done with that dataset alone, or in combination with other tree-ring datasets available in TRISH from the system administrators (TRISH team members) or from other users who have set access  to their contributed datasets to "Public."  Each uploaded dataset gets its own unique ID for further dataset management and use.

Submitting a new dataset is done by filling up, validating, and submitting the “Add New Dataset” form in the UDMT which is highlighted by peach background color in the illustration of the previous section. The form has 3 text inputs -

1. “Dataset ID”:        It is required and must contain alphanumeric characters only. We suggest a short meaningful word the user can easily associate with the dataset, e.g. “fieldwork_2023”.
2. “Dataset Name”: It is required and it should have a multiword description of the dataset, e.g. “Demo Middle Sites”. Note, the name of the dataset, will be used to list it in the “Select Tree-Ring Data” filter -
                           
3. “Dataset Comment”: It is optional and it can contain any text of reasonable length.

File chooser for -

1. “Sites Metadata File” - see section “Metadata file format” below for the data format of this file.
2. “Sites TR-Data File” - see section “Tree-ring data file format” below for the data format of this file.

Note, the size of this file is limited to about 1000 sites in the dataset. If a user needs to upload a larger dataset, it is recommended to contact any TRISH team member for assistance and manual transfer of the data to the system administrator.

Last form input is the radio button group for “Access Permissions” where a user can choose one of two options -

1. “Public” data access permission which makes the dataset visible and available for the reconstructions by any other registered user in the TRISH system.
2. “Private” data access permission which makes the dataset visible to the current user only.

Note, that the dataset permission settings can be instantly changed at any time, in the user data management form described in the “Managing tree-ring data” section.

After the form is filled up and upload files are chosen, the user can use one of the three action buttons at the bottom of this form -

1. “Validate” - It will check the following:

1. Format of the dataset ID string.
2. Uniqueness of the dataset ID, making sure it is not yet used in the system.
3. “Dataset Name” input is not empty.
4. Format of the sites metadata file. If the format does not  comply  with  the  required  standards,  the particular problem is likely to be identified by the  system  and  reported  back  to  the  user  for correction.
5. Same as (d) for the sites tree-ring data file.

If all the above checks are passed, the validation status will me displayed in the form’s right column as shown here-

2. “Validate and Save” - It will perform the validation check as described above, and will save the data to the TRISH system. When it is done, the “Add New Dataset” form gets cleared/reset and the dataset will immediately show up in the user data management form “Manage Uploaded Datasets” (described in the “Managing tree-ring data” section) and in the  list of the “Select Tree-Ring Data” filter illustrated here.
3. “Reset” - It will clear up and reset the “Add New Dataset” form.

Metadata file format

Metadata file has to comply with the following specifications -

1. It is a text (ASCII character set) tab or comma delimited spreadsheet file.
2. The header line is the first (top) line in the document.
3. Header names are case sensitive and cannot have front or back padding spaces. Double quote marks are allowed, but not required.
4. Required header names are -

Note, those inputs not marked as "Required" do not affect the analysis, but are  helpful for interpretation of output. "Species" is a four letter code (e.g., "PSME"), consistent with abbreviations in the ITRDB, "Type" is a one-letter code allowing the user to distinguish chronologies of data-types. The developers, for example, use R, E, L, and B for total width, earlywood width, latewood width and delta blue intensity, respectively.

5. Column order is arbitrary and the specific column order shown is not required.
6. Any additional columns are OK, and will be ignored/discarded by pushing the data to the system databases.
7. The spreadsheet template file for the site metadata can be copied from this link -
   Template for TRISH Tree-Ring Sites Metadata File
   If using spreadsheet template, be sure to save file as tab-sep or csv for upload to TRISH.

Table A. Example of the metadata file spreadsheet (required headers are indicated by bold font).

Tree-ring data file format

The Tree-ring data file has to comply with the following specifications -

1. It is a text (ASCII character set) tab or comma delimited spreadsheet file.
2. The first line can be a column numerator, some user comments, or anything the user wants to use it for.
3. The header line is the second from the top line in the document.
4. Header names are case sensitive and cannot have front or back padding spaces. Double quote marks are allowed in Header names but are not required.
5. Required header names are -

1. Year          It must be the first column.The values (years) must be in increasing order.
                    Values must be in integer format, e.g. 1957
2. Site IDs    One per each column, and identical to the Site IDs in the metadata file.
                   Order preferably (not required) is the same as in the metadata file described above.

6. The  tree-ring  values are assumed to be dimensionless site chronology indices in decimal number format (e.g., 1.00 is normal, or average). Chronologies can be either "standard" or "residual."  TRISH will optionally allow standard chronologies to be prewhitened to pseudo-residual chronologies  for use in reconstruction.
7. Nodata values for the tree ring data must be filled with the string “NaN”
8. The spreadsheet template file for the site metadata can be copied from this link -
   Template for TRISH Tree-Ring Sites Data File
   If using spreadsheet template, be sure to save file as tab-sep or csv for upload to TRISH.

Table B. Example of the tree-ring data file spreadsheet (required headers are indicated by bold font).

Data copyright statement

• The TRISH development team has made several public tree-ring networks available in TRISH  for testing and illustration purposes. The data source for those public networks is the International Tree-Ring Data Bank, whose data is subject to associated licenses and disclaimers (https://www.ncei.noaa.gov/archive).
• User datasets, titled in the input "Dataset ID" and shared with other TRISH users by selecting the “Public” option, are made available under the terms of the Creative Commons Attribution 4.0 International License (CC 4.0) license.

Managing tree-ring data

Usage

All previously uploaded user tree-ring datasets can be managed using the “Manage Uploaded Datasets” section of the UDMT tool -

First, the dataset that a user wants to manage needs to be selected by ID from the “Uploaded Datasets” list. When selected, the three following actions can be applied to it by using the corresponding action buttons -

1. Delete - the currently selected dataset in the drop-down selector on the left to this button will be immediately deleted from the system and will no longer be available for new Reconstruction Analysis.
   Note, this action cannot be undone.
2. Update - dataset name, comment, and access permissions can be modified and updated on the server:

1. “Selected Dataset Name” is a required string for a short description of the dataset that is used to list it in the “Select Tree-Ring Data” filter (see Illustration above).
2. “Selected Dataset Comment” is an optional text for the user about the selected dataset.
3. “Access Permissions” is a radio-button group to select and modify the availability of this dataset to other users of the system, for the Reconstruction Analysis.

3. Reset - this action restores name, comment, and access permissions for the selected dataset to its previously saved status on the server.

Questions and comments are welcome - alex.proussevitch@unh.edu

Written by Alexander Prusevich
Edited by Stanley Glidden, Richard Lammers, Alexander Shiklomanov,  and TRISH team members.