Publishing to GBIF

We automatically serve all live collections and some snapshot collections to iDigBio via DwC-A files . We also serve these same dataset to GBIF, but before we do, each institution must register with GBIF.

The ability to publish a dataset to GBIF from any Symbiota portal requires first that the “collection” manager set up an account with GBIF for their institution or collection, and then the collection uses the Symbiota portal for data users to harvest. GBIF needs to have this direct agreement with the institution housing the collection before Symbiota can make their data available to GBIF. This is a simple registration step on the side of GBIF, part of whose function is to ensure that institutions stay informed of where their data end up.  If your institution is already registered with GBIF, you can add your collection as another dataset and your simply need to be added to the agreement. You do not have to coordinate with other collections at your institution, you can publish your data separately.

Typically, all “live collections” in a Symbiota portal serve data to both GBIF and iDigBio, although “snapshot collections” may also serve their data to the public this way.  GBIF harvests data directly from the data provider, Symbiota simply allows GBIF to harvest directly from a data provider through their “collection” on a Symbiota portal.  GBIF  typically shows datasets (e.g., Symbiota collections) as sets from the institution. Each collection within an institution can have their own workflow for GBIF to harvest data if they wish, for example data from a vertebrate collection can come from Arctos via VertNet and data from the institution’s insect collection can be harvested from Symbiota (e.g., University of New Mexico). The workflow described below was developed by Tim Robertson (GBIF) and Ben Brandt (Symbiota).

GBIF Steps  (Contact helpdesk@gbif.org and Neil Cobb  if you need help navigating through steps)

  1. If you already have a GBIF Organization Key for your collection and the “GBIF user” specified in the Publishing Information box has permissions to create and edit datasets for your organization, then enter the key in the “GBIF Organization Key” box and click on the “Save Key” button. The GBIF Organization Key should have the following format: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
  2. If you have a GBIF Organization Key, but are unsure if we (symbiotascan) listed in the Publishing Information box (see below) has permission to make your dataset available to GBIF for your organization, contact GBIF helpdesk (helpdesk@gbif.org)  and request that symbiotascan be given permission. Once the permissions are set, enter the key in the “GBIF Organization Key” box and click on the “Save Key” button. The GBIF Organization Key should have the following format: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx
  3. If your collection does not have a GBIF Organization Key or you are uncertain if it does, go to the “GBIF Endorsement Request page”  and follow the instructions to establish your collection/organization with GBIF. Be sure to  look up your collection or institution with GBIF to ensure that it is not already established. In filling out the GBIF survey you do not need to use an IPT, instead you are publishing a DwC via the SCAN portal. You do not need help publishing, SCAN is publishing for you.
    1. If your collection is already established, review the GBIF metadata for your collection and existing datasets and contact GBIF to make any appropriate changes, if necessary. You may want to coordinate with other collections at your organization at this point, since the GBIF organization entry typically relates to your institution as a whole. If your collection already has data published with GBIF, review that data to ensure it is not the same data you wish to publish in the Symbiota portal. If it is, make the appropriate arrangements with GBIF to manage that data BEFORE publishing from the Symbiota portal.
    2. If your collection has not been established with GBIF yet, follow the instructions for requesting endorsement with GBIF to obtain a GBIF Organization Key. The GBIF Organization Key should have the following format: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx. Once your organization has a key, contact GBIF and request that the GBIF user specified in the Publishing Information box has permission to to make your dataset available to GBIF. Once the permissions are set, enter the key in the “GBIF Organization Key” box and click on the “Save Key” button.

Publishing Information box is only available to collection administrators: Go to your collection, click on pencil, go to Darwin Core Archive Publishing and go to Publishing Information box (below).

In the end you need a user account on the GBIF website and editor rights on that account. If you already have one please send them to the GBIF Helpdesk:

  • Account user name or email address
  • A list of the organizations that you will be publishing for (please submit a url to the GBIF publisher page)

 

Symbiota Steps

Once the collection is configured as a GBIF registry entry for your organization, then the GBIF checkbox will show up in each collections’ metadata page as well as the box for each collection to configure publishing for their collection in their Darwin Core Archive Publishing page. You can follow the steps below or simply contact Neil Cobb and we will complete these steps for you.

  1. Login to the portal
  2. Go to your collection’s Collection Profile page, click on the small pencil icon in the top right corner, and click on the “Edit Metadata and Contact Information” link in the Administration Control Panel box.
  3. On the Edit Metadata page, check the GBIF box to the right of “Publish to Aggregators:”, and then click the “Save Edits” button
  4. On the Collection Profile page, click on the small pencil icon in the top right corner, and click on the “Darwin Core Archive Publishing” link in the Administration Control Panel box.
  5. If a Darwin Core Archive has not already been published for your collection, you will first need to publish one by clicking on the “Create/Refresh Darwin Core Archive” button in the Publish/Refresh DwC-A File box.

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