Using EarthChem Portal to create a data table
EarthChem's web portal offers access to geochemical data in federated geochemical databases, including PetDB, GEOROC, NAVDAT, SedDB, the Deep Lithosphere Dataset, the USGS National Geochemical Database, MetPetDB, and the GANSEKI database. This page explains how to extract an integrated table of your desired geochemical data. The two main steps to getting your integrated dataset are:
- Constrain sample selection
- Choose the data display and geochemical parameters
1. Constrain Sample selection
Sample selection is set on the Portal Search page.
The sample selection can be constrained by:
Reference | Keyword | Sample ID | Location | Geologic Province
Ocean Feature Name | Volcano Name | Sample Type | Chemistry
Obtain samples that were reported in a particular reference (article, report).
- Author: should be an exact match of the last name (e.g. Shaw)
- Title: full title or title fragment
- Journal: full journal name or name fragment
- DOI: e.g.: 10.1016/0012-821X(95)00023-6
The keyword query searches a generic descriptor field contained in the EarthChem schema. This is a free-text field that allows the supported datasets to provide a descriptor of their own choosing. Most often, this field contains a short sample description providing the sample's location and composition. The keyword search also includes rock name in the queried results.
Sample IDs are the names used by the federated databases. The different databases have their own conventions, but if you have the sample ID from a particular database, you may search for it here. The sample name must be the complete name (not a fragment). The search will return samples with similar names, (common typos such as 1 for lowercase L), and dashes do not matter, for example, ML12 will return ML-12 and M112.
Some databases use a repeatable convention for unique sample naming, PetDB typically gives some combination of Ship, Expedition/Cruise (name or leg), station, and sample, for example,
Ocean Drilling Program, leg 176, hole 735B, core 1R, section 1, 35-37 centimeters
You can set the location in four different ways.
- Define a polygon by clicking on an interactive map
- Choose a terrestrial location using a text-based gazetteer.
- Define a bounding box with N, S, E, W boundaries
- Define a polygon with longitude/latitude pairs
After you set your constraint and click the Submit button, the query page will show a map of your area of interest.
To select a geologic province, select a province from the list, view the map outline, then click the Submit button to set the constraint. All geologic province definitions come from the Global GIS dataset from American Geological Institute and the USGS.
Ocean Feature Name
To select an Ocean Feature, select an ocean feature from the list, view the map outline, then click the Submit button to set the constraint. Ocean feature polygons were defined by EarthChem.
To select samples from a given volcano, choose from a list of volcano names from the Global Volcanism Program of the Smithsonian Institution. Select a volcano name, view the location in a map, then click the Submit button to set the constraint. You will also be able to follow a link to the Smithsonian volcano page for more information.
Under sample type, you first choose among a list of general rock types. Next, you will have the option of choosing a more detailed rock type (e.g. gabbro, amphibolite).
For Igneous and Sedimentary categories, there are more customized choices.
- Names assigned by collector or author: These names are the collector-assigned name in the publication, regardless of the chemical composition.
- Names calculated from chemistry using TAS classifications (for igneous rocks): TAS stands for Total Alkali Silica, the classification system assigns names to volcanic rocks based on the relationship between the combined alkali content and the silica content. This classification is determined by the chemical composition of the sample and disregards the author-given classification.
- Names from EarthChem Categories: EarthChem categories are a standardized naming convention that maps author-given names like "granite" to a standardized, hierarchical vocabulary e.g. "igneous>plutonic>felsic>granite".
To constrain samples by chemistry or CIPW norms (a calculation based on the typical minerals that may be precipitated from an anhydrous melt at low pressure), first locate the parameter of interest, then click on the box for "exists". This will automatically fill in the range 0 to 100% in the boxes and will return samples with any value measured for that parameter. If you want a narrower range, enter the lower and upper bounds of the WT% that you are interested in (e.g. 0 to 30%). This sets the constraint to return samples that have a measured value between the minimum and maximum of the parameter.
If you want to set constraints on more than one parameter, click AND or OR to combine the constraints.
2. Choose the data display and geochemical parameters
Once you have set all of the constraints on the samples, click “Continue to Data Selection.” You will see a number of different options for accessing the data, metadata, and visualizations. For more information on the visualization tools, see the page on additional EarthChem Portal features.
To proceed to the integrated dataset, click on the first option “Get Chemical Data.” You will see a list of the chemical parameters stored in the EarthChem Portal, grouped by type (Major Oxides, Isotope Ratios, Rare Earth Elements, etc.)
You may customize your output table by setting the following options:
- Samples to Display: The default option is to show samples only with measurements for the checked parameters ("Show samples with any of the checked values defined."), but you can also set the display to only samples that have ALL checked values defined, or ALL samples returned from your original query.
- File Type to Display: The default option is to display an HTML table, but you can also download a text file or a Microsoft Excel spreadsheet.
- Output Format: The default option is to show one row per method (a sample may have multiple rows), but you can choose to display one row per sample, which will give you the additional options to display Units and Method in additional columns.
- Choose Chemical Data to Display: The default option is to Show Standard Output Items (a set list of chemical parameters - the list of parameters, click here), but you can choose to show all of the checked parameters. Note this is different from setting "Samples to Display." The samples are selected in item #1 above, and now there is the option to display only a subset of the chemical parameters.
Finally, click the Go To Data button. The click will either display the HTML page or download the .txt or .xls to the default location in your local machine.