AusGeochem Help

 

AusGeochem is a bespoke, open data platform for the geochemistry community. Developed by the AuScope Geochemistry Network (AGN) and partners Lithodat, AusGeochem enables users to visualise, synthesise, disseminate and extract geochemistry data in a global geospatial context.

This help guide includes a series of instructions and tutorial videos designed to assist users navigate the many features of the AusGeochem platform.

1 — Getting Started

a) User Registration: General Users and Data Contributors

Registering as a General User for AusGeochem is a simple and fast process, requiring you to simply provide your name, email address and password, and accept the AusGeochem Terms of Use. General Users can explore, interrogate, and download all publicly visible data in AusGeochem and make use of the platform’s built-in data visualisation and synthesis tools.

To be able to upload data into AusGeochem, users must first upgrade their account to Data Contributor. This involves simply providing a few bits of additional information, such as the academic, government or professional institution that you are associated with, your group/team and role, institutional email (if not already provided upon General User registration) and your OrcID. If you do not already have an OrcID, you can easily and freely obtain one here. Data Contributors can upload, disseminate, and publicise data within AusGeochem, as well as browse the data of their institution and its community.

b) User Interface Overview

The AusGeochem User Interface (UI) consists of two primary elements, the main Map View in which data can be geospatially explored and My Data, where Data Contributors can manage their data. In addition, users can manage their account details under the Account tab, and obtain information about the platform, get help, provide feedback, report bugs, view tutorial videos and view the Application Programming Interface documentation via the Help tab.

2 — Data Consumption

a) Viewing, Analysing and Downloading Data in Map View

AusGeochem users can view, analyse and download geosample metadata and associated geochemistry data from within Map View, which they control via the green buttons on the left-hand side. There, Users can select which datasets (called Data Packages in AusGeochem) and data types they wish to view via the Data Packages and Layer Selection buttons, respectively. Using the Base Maps button, Users can select from a range of base layers, such as satellite, streets, geological map, dark- or light-coloured maps.

The global geospatial database can be explored in Map View in much the same way as Google Maps, by clicking and dragging your mouse. The map can be zoomed in or out using the “+/-” buttons in the bottom-right corner, your mouse scroll wheel or via pinching gestures on your laptop trackpad. The angle of perspective can be adjusted by holding the Control button and clicking and dragging your cursor.

Users can retrieve geosample information and associated geochemical data for an individual sample by clicking on a sample locality on the map. Alternatively, Users can use the Multi-Selector tool to view and synthesise multiple samples and their associated data simultaneously. With the green Multi Selector button selected from the left-hand side, simply click out a polygon over the area of interest, double-clicking to close the polygon. A pop-up window synthesising and listing the selected data will then appear, from which different data dashboards can be selected using the Analytical Plots drop-down menu. Within the dashboards, synthetic plots and detailed tables can be generated and downloaded, as well as a list of references associated with the selected data.

b) Filtering and Downloading Data in My Data

Data can also be explored, filtered and downloaded in My Data. After selecting the type of data you wish to explore via the list of data types on the left-hand side, the database can be explored using the search field and applied filters of your choosing.

3 — Data Contribution

a) Creating and Managing Data Packages

Datasets, whether they be mineral and rock geosamples metadata or associated geochemistry analyses, are uploaded in Data Packages via the My Data tab. Data Packages are created under the Data Package tab of My Data. Data Contributors control data privacy on a per Data Package-basis. Data Contributors have the option to share the data with the whole community (public), share the data with selected collaborators or keep unpublished data private.

The private option is intended to keep data out of the public view for a limited embargo period. Since AusGeochem is designed as an open repository, there is a limit of two years from the date of data upload during which a user may nominate to keep their data private. By default, data uploaded to AusGeochem will be set as publicly available unless changed by Users. Data that already exists in the public domain, such as those in published scientific journals, must be uploaded as publicly available datasets.

Account-holders will receive notification that data held in private mode will be automatically converted to public mode at the end of the two-year period. Upon receiving this notification, the Account holder can request an extension of the embargo period for an additional 1 year, which will be granted automatically.

At the conclusion of this initial extended embargo period, an additional extension to the embargo period can be requested in writing (totalling a 4-year embargo period). After the end of the 4-year embargo period, any data which was kept private will be made publicly available through the platform.

b) Creating and Uploading Data on an Individual Basis

The AusGeochem platform owes its utility and flexibility to the relational architecture of its database. In it, all data are related to one another via a series of structured relationships, which can be used to query the database and perform on-the-fly synthesis, visualisation and analytics. To maintain these logical connections between data of various types within AusGeochem, data must be uploaded into their corresponding tables. For example, geosample metadata are uploaded into the Samples table, literary references into the Literature table, secondary ion mass spectrometry (SIMS) U-Pb data into the U-Pb SIMS Data table, and so on. Data Contributors can upload data of all types, with the exception of Rock and Mineral types, on an individual basis via the “+ CREATE” button on the associated tabs in My Data.

c) International Geo Sample Number (IGSN) Minting

AusGeochem Data Contributors are highly encouraged to mint International Geo Sample Numbers (IGSNs) for their uploaded geosamples. These unique alpha-numeric codes provide a means for consistent identification, citation and localisation of physical samples, and help prevent duplication in the database. Data Contributors can choose to automatically mint IGSNs for geosamples upon upload, or at any subsequent time via the Samples tab in My Data. Each IGSN minted sample is given a dedicated webpage, QR code and citable DOI.

d) Batch Uploading Data

Most data types can also be uploaded in bulk via dragging-and-dropping a populated AusGeochem CSV file template. Downloadable blank CSV templates for these data types can be found under the Drag-n-Drop window at the bottom of their associated tab in My Data..

e) Contributing SIMS U-Pb Data

Uploading SIMS U-Pb Data can be done via a wizard which enables users to drag and drop a standard or AGN-template SQUID3 CSV output file in the Drag-n-Drop window at the bottom of the U-Pb SIMS menu in My Data. The wizard takes you through the data uploading process step-by-step and helps you link data to existing samples and archive the data reduction method applied.

A batch upload is also available where any U-Pb SIMS data set can be uploaded by populating a preformatted CSV file and returning it to the batch uploader.

If need be, a raw SIMS data file can be uploaded and associated to samples which can then be accessed by collaborators or future users.

4 — Application Programming Interface (API)

The AusGeochem Application Programming Interface (API) endows the platform with enormous potential by allowing users to expand on the existing capabilities of the platform to fit their data needs. Through the API, external software components, operating systems, and applications can access and interact with AusGeochem-hosted data to facilitate a variety of tasks, including automatic machine-to-database metadata upload, automated data retrieval, and the incorporation of additional data synthesis functions and machine learning algorithms.

5 - How to Cite

How to Cite the Platform:

Publications and reports that have benefited from the use of AusGeochem and its archived data should reference the following papers.

For general AusGeochem platform use, please cite:

Boone, S.C., Dalton, H., Prent, A., Kohlmann, F., Theile, M., Gréau, Y., Florin, G., Noble, W., Hodgekiss, S.A., Ware, B. and Phillips, D., 2022. AusGeochem: An Open Platform for Geochemical Data Preservation, Dissemination and Synthesis. Geostandards and Geoanalytical Research, 46(2), pp.245-259. doi: 10.1111/ggr.12419

This paper is open access and can be viewed here.

For work which utilises thermochronology data (fission track, (U-Th)/He and thermal history models) and associated analytical tools, please cite:

Boone, S.C., Kohlmann, F., Noble, W., Theile, M., Beucher, R., Kohn, B., Glorie, S., Danišík, M., Zhou, R., McMillan, M. and Nixon, A., 2023. A geospatial platform for the tectonic interpretation of low-temperature thermochronology Big Data. Scientific Reports, 13(1), p.8581. https://doi.org/10.1038/s41598-023-35776-3

This paper is open access and can be viewed here.

 
 

NEED MORE HELP?
Please reach out anytime if you need assistance, someone from the AuScope Geochemistry Network (AGN) team can help you — please email us