Important Announcement

Updates to the AmphibianDisease Portal

Changes are coming!

Summary of what’s new: AmphibianDisease portal is partnering with Geome-db to deliver improved services. In Phase One, behind the scenes we’ve improved the validation process to ensure data meet the proper data standards. Phase Two will upgrade the website and streamline its interface, including updates to the Data Dashboard. A new search and mapping interface will replace the mapping functions. Look out for improvements and new tools to access and analyze Bd and Bsal data in the coming year. For some functions, there will be temporary re-directs to Geome-db.org, where we are sharing database functions.

The Amphibian Disease portal has important and exciting changes to announce! We are now collaborating with Geome-db.org for validation and data services! Geome-db is the Genomic Observatories Meta-Database, which is a web-based database that captures the who, what, where, and when of biological samples and associated genetic sequences. Geome-db ensures the metadata from bio-samples are discoverable, accessible and useful in research by adhering to global metadata standards and by providing multiple ways to access data. It is currently supported by the Berkeley Natural History Museums (BNHM), Smithsonian National Museum of Natural History, and NSF’s iDigBio efforts.

While we are making these upgrades and changes, the Amphibian Disease portal may have reduced functions temporarily; apologies in advance as well as thanks for your patience. It will be worth it! For more information, please contact amphibiaweb@berkeley.edu.

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What is changing? We are planning two phases of updates. Phase One, which is now mostly complete, is primarily in the backend database where data, projects, and user accounts have migrated to Geome-db. Originally, the Amphibian Disease portal used an earlier version of the Geome validation service (known as FIMS), which has now been deprecated. Adopting and using the same validation process as Geome-db will allow a streamlined way to maintain security and share enhancements from the GEOME project. See how the two projects line up in the table below. Phase Two are updates to the main website at amphibiandisease.org to bring enhanced query and data dashboard pages, updates to the documentation, and other updates for a more streamlined and uniform user experience. Technically, Phase Two will migrate our current web site platform to Hugo, an open-source website generator, which will make new development easier in the future. We plan to start in earnest in January 2020.

Why the change? The database changes will allow new enhancements, better stability and security, and most importantly, make it easier for the AmphibiaWeb and BNHM team to keep the site up and running. We also will update the public website for the Amphibian Disease portal to provide a more uniform and robust user interface, which will also make the website easier to use. These changes will allow us to anticipate future projects and development.

What will remain the same? We are still committed to the same mission and functions on which the Amphibian Disease portal were built— Our mission is to serve as a repository for Bd and Bsal data from field and biocollection samples and thus aggregate, visualize and share data to enable understanding the disease dynamics of this major cause of amphibian declines worldwide. Amphibiandisease.org aims to be the central portal for Bd and Bsal data.

Impacts to the Amphibian Disease portal user: New users will be redirected to Geome-db.org to register for an account. Once logged in, users can select the AmphibiaWeb Disease portal team, create a project, download a template and upload data, select public and private status, just like in the Amphibian Disease portal. New data will be available on the Amphibian Disease portal at amphibiandisease.org.

Comparison table of Amphibian Disease portal to Geome-DB

Amphibian Disease Portal Geome-DB
Equivalent to the portal’s home interface at amphibiandisease.org Within Geome-db, now organized as a Geome Team; once registered, users can select “AmphibiaWeb’s Disease Portal” team to download template, register a new or access an existing Project
Log in procedure Redirects to Geome-db.org; new users register here.
Project Pages Same as Geome Projects
- Able to upload via template - same
- Able to add people to your project - same
- Assigned citable DOI - same
- Uploaded data validated for data quality, metadata standards, taxonomy - same
Datasets of samples Expeditions
- Uploaded spreadsheets of data, based on a single trip or single experiment - same
- Able to replace or add new data - same
- Able to be public or private - same

Reference websites:
https://amphibiandisease.org
https://geome-db.org/about

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