Help

Need Help?

Welcome to G.E.M.S, a platform for improving interoperability, sharing, and analyzing data. To do any of those things, a user will first need to login. Once that prerequisite is satisfied we can get started.

Steps

If a user has their own data that they wish to put in their workspace they will need to upload it. We have several options available as described here. To find data that the user has been granted access, or is discoverable and available to request access, use the search page.

Register a File in G.E.M.S

After you’ve uploaded your file to the GEMShare server and decided you want to share it with others, your next step is registering the file. Registering makes GEMShare aware of the file so you can grant access to people, teams, or the world. It also allows you to add useful metadata that will not only help others find the file, but make it more interoperable with other data and help people use it more effectively.

Registering a file generally takes two steps: Select the file Enter metadata for the file If the file contains columnar data, there are four additional steps that can help make your file more usable by others: Confirm the delimiter and whether the file contains column headers Edit column names and add notes to each column to aid understanding Match columns to industry standard terms to aid interoperability Use data cleaning tools to help solve spelling errors and inconsistencies, find outliers, etc. Select a File Select a File This page shows your home directory on the GEMS server. Browse to the file you’d like to share and click it. If your file has columnar data in it, GEMS will help you provide metadata about the columns (see steps 2 through 5). If your file does not have columnar data you can immediately enter metadata about your file (skip to step 6).

File Delimiter and Column Headers

File Delimiter and Column Headers GEMS will guess about the delimiters in your file and whether the first row of the file contains column names. If it guesses incorrectly about any of this you can change it here. If the first row of your file does not contain column names GEMS will use simple sequential names (column1, column2, etc.) for your columns, which you can change to more useful names on the column metadata screen. Column Metadata Entry Column Metadata Entry You can change the names of any of the columns in your file on this page. This will not make any changes to your file. It will only change the column metadata that is included with it. You might have column names that are acronyms whose meaning may not be obvious organization-specific terms that may have more widely recognized alternatives arbitrary and not related to the data (column1, column2, etc.) Changing these names to more useful and recognizable names will help those who find your file more easily work with it. You can add helpful notes for any of the columns in your file. This could be things like: unit of measurement special calculations required to arrive at these figures method(s) used to gather the data for this column

Column Ontology Match

Column Ontology Match Using files from disparate sources on the same project is part of what GEMS is meant to enable, and one of the ways we encourage interoperability is by helping you link common concepts in different files using industry standard terms. On the ontology match screen you can match each of your columns to industry terms from several domain-specific ontologies (ten as of this writing, though more are planned). When the page first loads you’ll see that GEMS has already filled in an ontology match in cases where there was an exact match with your column’s name. These are just initial suggestions, and you are free to change these. There are two ways to change the matched term for a column: If the term in the Search box for the column is correct, clicking on the box in the Ontology Term and Source column will bring up a selection list. Find the term that best matches the column from your file and select it. If the term in the Search box for the column doesn’t reflect the nature of the data in the column or the current search term didn’t return any results, you can search for other terms by typing in the Search box and selecting from the updated results.

Spelling Corrections

Some columns in your file might have subtle variances in how the same values are presented (capital vs. lowercase, minor spelling differences between regions, etc.). GEMS will provide spelling suggestions for columns that are eligible, and can even make the suggested updates to a new copy of your file. This will not alter your original file. To view the spelling suggestions, click the Select Corrections... button for the column whose suggestions you’d like to see. Spelling Recommendations The Spelling Change Recommendations dialogue box shows each instance of a potential misspelling in a column, the alternative recommended spelling, as well as how many times each spelling appears in the column. If you would like GEMS to create a new file that features spelling recommendations you have accepted, click the Select Corrections... button for each column, select any spelling updates you’d like, then click the Save Changes at the bottom of the dialogue. Save Corrections When you’ve completed your selections, click the Correct Spelling button and all the changes you specified will be made in a copy of your original file (your original file will not be altered).

This new corrected file will now be the file you are registering. File Metadata Entry File Metadata Entry The file metadata entry screen is the place to enter general information about your file as well as any relevant domain-specific qualities. General information includes not only the basics but things like keywords that will help people find the file, the date range that is covered by the file, any intellectual property rights that apply, etc. What you enter on this screen is meant to help people: Find the file Understand how to use it (file format, delimiters, image compression, etc.) Understand its context (time period, geographic region, methodologies used, etc.) If you are unsure of how to fill in a specific field or what the term means, click the blue question mark next to the field name for a brief description.

After a product has been registered it can be freely shared with users and teams. The permissions or privileges available for sharing data products are:

  • NONE - Allows the user to see the metadata of the product, but not the product itself
  • READ - Allows the user to access the data
  • ADD - Allows the user to register a new product as a derivative of this product
  • EDIT - Allows the user to add new versions of this product
  • DELETE - Allows the user to delete this version of a data product
  • MANAGE - Allows a user to change user and team privileges with regards to the product.

Open an Analysis Environment Getting access to third party data is really helpful, but users will probably want to work with it before downloading it. In some cases users will be able to do everything they want on G.E.M.S, in others users may want to simply explore data before downloading with Globus. In either case, G.E.M.S provides the ability for users to have an isolated compute environment as a Docker container with a personal workspace. Users that prefer Scala or Python G.E.M.S can use Jupyter notebooks, users preferring R can also use either Jupyter or R Studio, or users that have UIs that are compatible with Linux can use the remote desktop environment. All of these environments have been built with common GIS libraries such as GDAL and GRASS included.

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GEMS is an international agroinformatics initiative jointly led by the College of Food, Agricultural and Natural Resource Sciences (CFANS) and the Minnesota Supercomputing Institute (MSI) at the University of Minnesota. GEMS® is a registered trademark of the University of Minnesota. GEMSOpen™, GEMShare™ and GEMSTools™ are trademarks of the Regents of the University of Minnesota.