Publishing Occurrence Data to GBIF

Before a Symbiota portal instance can publish to GBIF, the portal manager needs to register the portal as a GBIF Publishing Installation. Once the portal is configured as a GBIF publisher, collection managers will have the ability to publish their occurrence data directly from the portal to GBIF, similar to how data can be published from an IPT installation. Collections being managed as “live datasets” within the Symbiota portal can often immediately publish to GBIF and iDigBio without issues. Collections that make use of an in-house management system (e.g. Specify, Ke-Emu, etc.) and only publish a snapshot of their data within a Symbiota instance may also use the portal to publish GBIF, but only if: 1) they are not publishing their data through another means (e.g. IPT installation, VertNet, etc.), and 2) an occurrenceID GUID is included in the data being pushed from their in-house database to the Symbiota dataset. If the collection is using the Symbiota publishing tool built into Specify, the occurrenceID GUID will be automatically included in the data upload from Specify.

Publishing Collection Dataset from Symbiota Portal – This step is done by collection managers after the Symbiota portal has been configured to a GBIF Publishing installation (details below)

1. Collection managers first need to set up an institutional account with GBIF so that there is a direct publishing agreement established between GBIF and the institution. The institutional account will be used to list multiple collection datasets associated with that institution (e.g. https://www.gbif.org/publisher/4c0e9f60-c489-11d8-bf60-b8a03c50a862), and thus the collection manager should coordinate with other collections within their institution. Note that the different datasets listed under a single institution can be imported using different publishing sources. For instance, the zoological collections could import their data from VertNet (http://ipt.vertnet.org) or an institutional IPT, vascular plant data from the SEINet (http://swbiodiversity.org), and lichens from Consortium of NA Herbaria (http://lichenportal.org). Use the GBIF Endorsement Request page (https://www.gbif.org/become-a-publisher) to register your institution. Use the organization lookup on that page to make sure your institution is not already registered. a. If you are sure your institution is not yet registered, complete the registration form and follow the instructions provided by GBIF. b. If your institution is already registered, review the GBIF metadata for your organization and existing datasets and contact GBIF to make any necessary changes. Be sure that none of the existing datasets contain the same data you are trying to publish. If they do, make the appropriate arrangements with GBIF so that the old dataset can be archived BEFORE re-publishing the new dataset.

2. Login, go to your collections Management Menu (via My Profile => Specimen Management tab => click your collection name), and click on “Edit Metadata and Contact Information” link in the Administration Control Panel. Verify your collection name and description (these will be used within the GBIF page), check the GBIF box to the right of “Publish to Aggregators”, and click the “Save Edits” button. If you don’t see a GBIF publishing checkbox, contact your portal manager and ask them to configure the portal for GBIF publishing.
3. Return to the management menu and click on the “Darwin Core Archive Publishing” link in the Administration Control Panel. Click “Create/Refresh Darwin Core Archive” button to package up your data within a Darwin Core Archive data package.
4. From within the Darwin Core Archive Publishing page, the GBIF user account registered within the portal instance will be listed and highlighted within the Publishing Panel. You will need to send this login to GBIF ([email protected]) along with a request for that user to be given permission to create and update datasets for your institution.
5. Once you receive an email stating that the permissions have been assigned, enter your institution’s GBIF publication key within the Darwin Core Archive Publishing page. The GBIF Organization Key should have the following format: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx (e.g. 4c0e9f60-c489-11d8-bf60-b8a03c50a862 for https://www.gbif.org/publisher/4c0e9f60-c489-11d8-bf60-b8a03c50a862). Click Verify and Submit Data button (some Symbiota installations will only show a Save Key button, which will verify and submit data). A link to your GBIF dataset will be displayed. It may take an hour or so for your data to be indexed and displayed.

Configure a Symbiota Portal as a GBIF Publisher (done by portal manager)

1. Contact GBIF ([email protected]) and request to set up a new Symbiota Installation (e.g. https://www.gbif.org/installation/ac2ad091-91eb-482d-a73f-061744da5dbf, https://www.gbif.org/installation/2c733a9d-363d-4d66-9aef-3e0f7bc44bec). Installations need to be associated with an existing publisher host (https://www.gbif.org/publisher/a86e9e36-12ec-49a4-a94c-c0c981fffb71, https://www.gbif.org/publisher/b648db34-3bf9-45eb-a65b-8176a3c3be88) or a new host will need to be created.
2. GBIF will ask you to create a new GBIF user account, which will be associated with your GBIF Symbiota Installation. Send the new login name to GBIF and request that they give the account the necessary permissions to create a new Symbiota GBIF Installation under the host from step #1.
3. Update the portal’s $DEFAULT_TITLE within the Symbiota configuration file (synbini.php), which will be used as the title of your GBIF installation. The default title is used within the of your portal’s webpages. It’s also placed within your EML file of your DwC-Archive data files as the organizationName of the metadataProvider, and thus used by GBIF as the title of you GBIF installation page.
4. Within the config file, enter the login name, password, and the host organization key (format: xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx) under the following variables. a. $GBIF_USERNAME = ''; //GBIF username which portal will use to publish b. $GBIF_PASSWORD = ''; //GBIF password c. $GBIF_ORG_KEY = ''; //GBIF organization key hosting the portal
5. A new Symbiota Installation will be created once a dataset is published from the portal. After the installation is created, send GBIF a short description of the portal.