Data Submission Manual

1. Log into Ag Data Commons or register for an account.
2. Go to your "My Data" link in the upper right of the screen.
3. Request storage for your data materials using the "request more storage" link
4. Choose the "+Create a new item" button in the upper left of the screen or use the "Upload" button in the upper right to initiate the drag and drop interface to add a file or folder.
5. Complete the form with information about the data.
   • Essential information includes Title, Item Type, Authors, Categories, Keywords, Description, Funding, License, Data Contact Name and Email, Publisher, Temporal Extent Start Date, Theme, Geographic Coverage (if answer to Theme is "geospatial"), ISO Topic Category, Bureau Code (for ARS data), Program Code (for ARS data), National Program Number (for ARS data)
   • Link any publications related to the data.
   • Upload or link data file(s) at the top of the form.
6. Save changes and when ready submit the dataset for review using the red "Submit for review" button on the right-hand side of the screen.

A user account is only required to submit data resources to the Ag Data Commons. Those wishing to view or download data do not require accounts.

To submit data resources, select "Log In" at the upper right corner of the Ag Data Commons home page. You will be prompted to select the user type for your account. Options include:

• Customer: Use this option for non-federal users (e.g., university partners, grant recipients, etc.). You can use Login.gov or eAuth to log into your account.
• USDA Employee/Contractor: Use this option if you work directly for the USDA. You can use your PIV card, USDA MobileLinc, or USDA Work Account through Microsoft to log into your account.
• Other Federal Employee/Contractor: Use this option if you work for a federal department outside the USDA. You can use your PIC/CAC PIN or Login.gov to log into your account.

Most users will start out with zero storage capacity and need to request additional capacity from the curation team to upload dataset files. To request storage, navigate to the "My Data" tab at the top of the screen. Below the tabs, in the center right is a bar displaying the total storage capacity for the user's account in the Ag Data Commons. Choose the link that says "request more storage" underneath the display bar.

This link opens a window that shows the user’s current storage quota and allows them to request storage space. Only request as much storage as needed for the material that will be uploaded directly to the Ag Data Commons. In the "add your reason and comments here (optional)" field, let the curation team know how many datasets you plan to upload and any other pertinent information to justify the increase in storage space. Choose the "Submit" button to send to the curators.

After submitting the request, the text under the storage capacity will change to "pending storage request" which means a curator has been notified of the request. Granting an increase in storage space can take up to 24 hours to fulfill, and possibly longer for larger storage requests.

Complete the registration and storage request process to begin submitting data files.

Before beginning your Ag Data Commons submission, decide how you want to organize your data. Does your data consist of multiple unique sets of data, or only one dataset containing multiple files of data? Try to imagine a data user to determine the most useful grouping for the data in question.

Create multiple Ag Data Commons records if:

• There are enough differences among the data files that they require unique descriptions of methods and data dictionaries (i.e., lists of the measurements included in the files).
• People would use and cite portions of the data independently.
• The authorship or publishers vary from dataset to dataset.

If creating multiple records, note relationships among datasets and other content using the Related Materials field relationships like "IsPartOf" if the dataset you create falls under a larger umbrella dataset, and "Cites" for datasets that draw material from existing sources (see more in the Related Materials field section of this page). In this way, users can create separate but related records for data that appropriately reflect the nature and connections between data.

Create a single record if:

• It would be confusing and redundant to generate several unique Ag Data Commons records where one will suffice.
• You cannot reliably and repeatedly separate distinct data files or datasets out from a larger database. In this case, create a single record for the whole database.

Another way to group multiple records is to create a collection of datasets. See the "Create a collection of datasets" section for more information.

To create a new dataset record, use the following steps as a guide:

• Select "Log in" at the upper right corner of the Ag Data Commons home page.
• Go to your "My Data" link in the upper right of the screen.
• Choose the "+Create a new item" button in the upper left of the screen.
• Proceed to populate the information fields on this page. Fields marked with a red asterisk must be completed for publication in the Ag Data Commons. See the Description of fields section of this page for a list of all available information fields.

When creating a record in the Ag Data Commons, users can upload data directly or link to data held elsewhere. The data uploaded directly receives a Digital Object Identifier, which provides a persistent link to the data. The catalog records linking to data held elsewhere receive a Handle identifier.

• To upload files directly to the Ag Data Commons for storage and preservation, use the field at the top of the web form and choose "Add Files". You can browse for the files or drag and drop from a directory on your computer. You can upload a zipped directory of files or individual files as you see fit.
  • Your combined uploaded files across all your datasets must not exceed 20GB to add data files using this method. To check your available storage capacity, navigate to the "My data" page and look at the bar in the upper right next to the search bar to determine how much of your allotted storage you have used to date. The amount you have used appears to the left of the bar, and the total storage available to you appears to the right of the bar. To request additional storage capacity, contact NAL-ADC-Curator@usda.gov.
• To create a catalog record that links to data files held in a different storage location, use the field at the top of the web form and choose "Link to external files". You can then enter a URL for the location of the files in the provided field. Click the check mark next to the field to save.
• Include your data dictionary as an upload with the rest of your data files or use the Related Materials field described further down the page to link to an existing data dictionary using the "IsDescribedBy" relationship.

When you navigate to the "+Create a new item" page to create a new dataset you see the following fields. Essential fields marked with an asterisk. All other fields are optional but encouraged. Performing a page search by using Control/F (PC) or Command/F (Mac) will highlight the field in question. 

Include the following in the narrative Description field of the dataset, if applicable:

Some of the following items have dedicated fields that allow for more detail. Including these details in the dataset Description field in addition to subject-specific fields may improve search and discovery.

• Make sure the Description describes the data, not the project or article
• Description should address the who, what, where, why, and how of the data
• Description of the experiment setting: location, influential climatic conditions, controlled conditions (e.g., temperature, light cycle)
• Processing methods and equipment used
• Study date(s) and duration
• Study spatial scale (size of replicates and spatial scale of study area)
• Level of true replication
• Sampling precision (within-replicate sampling or pseudo replication)
• Level of subsampling (number and repeat or within-replicate sampling)
• Study design (before–after, control–impacts, time series, before–after-control–impacts)
• Description of any data manipulation, modeling, or statistical analysis undertaken
• Description of any gaps in the data or other limiting factors
• Outcome measurement methods and equipment used
• Include a description of the individual files included in the package with file names, titles, and other relevant information about the package contents (if not creating a README file for this purpose)

Data description pointers based on information from the following publication:

Haddaway, N. & Verhoeven, J. (2015). Poor methodological detail precludes experimental repeatability and hampers synthesis in ecology. Ecol Evol, 5(19), 4451-4454. http://dx.doi.org/10.1002/ece3.1722

When logged in and viewing the "My data" tab, you can see all the content you created in the Ag Data Commons. The "Status" column on this page indicates the visibility of the dataset. A blank, or a gray circle indicates an unpublished dataset. A hollow green circle indicates an unpublished dataset in review by the curation team. A solid green circle indicates a published dataset viewable by anyone. Only the logged-in dataset owner can view their unpublished datasets.

Users can generate private links to unpublished content by choosing the dataset to share from the "My data" tab and navigating to the Edit page. On the right side of the screen in edit mode, choose the "Share with private link" option to generate the link to send to collaborators, journals, and anyone else who needs to view an unpublished dataset.

A dataset draft remains hidden from public view until a curator reviews and publishes the dataset and resources. Submit dataset drafts for review after you are finished editing so a curator may approve and publish them. Submit datasets for review in one of two ways.

Submit one or more datasets for review from the "My data" page

Submit multiple datasets for review at the same time using this workflow once the datasets need no further editing.

• Choose "My data" in the top right of the screen to see all the logged-in user’s datasets.
• Choose the checkbox to the left of all datasets to submit for review. Then choose the "Actions" button at the top of the list and use the “Submit for Review” option from the dropdown list.

Submit a single dataset directly during the editing process

This method makes the most sense for submitting a dataset for review immediately after editing.

• Enter the edit mode for the dataset in question through your "My data" page and make changes to the dataset as needed.
• When finished editing, choose "Submit for review" on the right side of the screen to move the dataset into the queue for moderation.

An Ag Data Commons curator reviews all submitted datasets and resources. Curators approve datasets for publication and inform submitters of any necessary changes prior to publishing. Curators may add keywords or other elements to enhance search and discovery in the Ag Data Commons.

If a user needs to add data or other resources to a dataset record after publication, navigate to the record in the "My data" page and edit the dataset as needed. Changes to datasets that will trigger in-record versioning include changes to the title, authors, license, adding new files, removing files, replacing files, or replacing the link to data files stored elsewhere.  See Figshare’s versioning policy for more details. Minor changes to elements like keywords or linked related materials will not trigger a new version.

The dataset owner can always edit a dataset’s content after submitting for review, as well as after publication. Re-submit the dataset for review after editing so a curator can approve and publish the changes.

Prior to publication, users can delete unwanted draft content using the "Delete item" option but cannot delete content once it has been published. Contact the Ag Data Commons curation team if published content must be hidden or removed.

The Ag Data Commons allows registered users to create collections of datasets which can receive a DOI for citation.

To create a collection:

• While logged in to your account, navigate to the Collections tab at the top of your screen.
• Use the "+Create a new collection" button at the top left of the screen to start a new collection or choose an existing collection to edit.
• If creating a new collection, fill out the web form. You will find fields like those available when creating a dataset.
• Use the "Save changes" button at the bottom of the form to save the metadata for the collection.
• To add datasets to a collection, choose the collection from the list in your Collections tab. This takes you to the collection where you will see the current group of datasets. To add more, use the "+Add new items" button in the upper left corner of the screen. Type the title of the dataset to narrow down options and then choose the dataset to add from the list by hovering over and clicking. A green checkbox appears in selected datasets, and you can choose multiple. When finished, choose the "Add selected item(s)" button at the bottom right of the screen.
• To share the collection without publishing, enter the collection and navigate to the "Manage" button with the gear next to it in the upper right. Choose "Generate private link".
• To edit your collection, enter the collection and navigate to the "Manage" button with the gear next to it in the upper right. Choose "Edit collection details" and make your edits.
• To reserve a DOI for a collection, enter the collection and navigate to the "Manage" button with the gear next to it in the upper right. Choose "Edit collection details" and scroll to the bottom of the form where you will select the "DOI Reserve Digital Object Identifier" option and save the changes.
• To publish a collection, enter the collection and navigate to the "Manage" button with the gear next to it in the upper right. Choose "Publish collection" if you have completed the essential fields. The published collection appears in the main Ag Data Commons dataset list so anyone can see and cite the collection.

General Submission Tips

✔ Spell out all acronyms and abbreviations.

✔ Check for typos.

✔ For data based directly on a paper, use the "Data from:" convention in the Title.

✔ Make the Title descriptive - Include locations, dates, and other informative text.

✔ Make sure the Description describes the data, not the project or article.

✔ Submit appropriate resources (data, not just figures or summary tables), preferably in a machine-readable format (csv is preferred for data files; XLS can be converted and added as an additional CSV resource).

✔ Provide a Data Dictionary and/or README file.

✔ Select "Preview item" from the right side of the screen to view the record as it will appear publicly.

✔ Choose "Submit for review" when ready to publish.