Amphibian Disease Portal

Important Annoucement

Tue, 17 Dec 2019 00:00:00 +0000

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

Can We Prevent a Second Amphibian Pandemic?

Sun, 19 Nov 2017 20:30:00 +0000

Photo of a juvenile Ensatina salamander. Photo credit: Tiffany Yap

When the fungal pathogen Batrachochytrium dendrobatidis (Bd) was first described in 1999, action was not taken rapidly, and a global amphibian pandemic ensued. We have since found that Bd has caused the declines and extinctions of over 200 species worldwide, and, as it continues to spread, numerous amphibian populations are constantly at risk. With the recent discovery of a second, closely related fungal pathogen, Batrachochytrium salamandrivorans (Bsal), and its presence in international trade, a second amphibian pandemic is looming. In an article published in EcoHealth, Yap et al. (2017) review what is known about Bsal - its biology, disease pathology, known distribution and susceptible species, diagnostic methods, and potential treatments. They discuss the global efforts to minimize its spread, highlighting the efforts of the Bsal Task Force, and they bring attention to regulatory gaps that impede a rapid response.

Proactive policy action was and continues to be an important step for amphibian diversity conservation. Almost two years ago the United States placed restrictions on salamander imports to prevent the spread of Bsal, and recently Canada followed suit. These actions seem to be benefiting local salamander populations; several published reports indicate that Bsal has not yet been detected in captive or wild salamanders in North America (Klocke et al. 2017, Govindarajulu et al. 2017). In addition, the United States Geological Survey has been conducting targeted surveys throughout the United States, and so far all salamanders have been found to be Bsal-free. While this is great news, salamanders are not yet in the clear.

Photo of an Oriental fire-bellied toad (Bombina orientalis), a close relative of the Yunnan fire-bellied toad (Bombina icrodeladigitora). Fire-bellied toads are popular in pet trade. Photo credit: Joseph Dougherty, M.D./ecology.org

Initially it was believed that only salamanders could be infected by Bsal; however, in April 2017 a study came out showing that captive midwife toads (Alytes obstetricans) could be infected and transmit the pathogen to cohoused salamanders (Stegen et al. 2017). Alarmingly, Bsal has also been found on Yunnan fire-bellied toads (Bombina microdeladigitora), both in the wild in Vietnam and in trade animals in Germany (Nguyen et al. 2017). This alternate pathway for Bsal to spread through frog vectors in trade poses a severe threat. The scientific community is now calling on the United States Fish and Wildlife Service to fortify their response to this crisis by extending a moratorium on all amphibian imports until a clean trade program is implemented to ensure that all trade animals are free of Bsal and any other disease.

Creating Projects, Uploading Data

Thu, 30 Jun 2016 11:43:59 +0000

Preparing to Upload Data

Creating Projects

The first step to uploading data is creating Projects. We describe the Project creation process in the documentation and once created, actual tested samples (the “data”) may be added later or by a collaborator.

Preparing the data

To facilitate organizing and uploading your sample data, we are partnering with the Biocode project. Their FIMS (Field Information Management System) provides a project-specific, ready-to-use XLS template, which can be generated and downloaded at their site:

Under Tools, select Generate Template

Choose the Project: Amphibian Disease

Select All fields or customize your own.

Definitions and DarwinCore standards, if applicable, are listed.

The XLS template

The downloaded XLS file will have several worksheets:

Instructions - simple metadata can be added here
Samples - where the data are entered. Do not alter field names
Data Fields - required and optional fields are defined, controlled vocabulary listed
Lists - controlled vocabulary for Samples. Do not edit this sheet!

Shortcut to download the complete XLS template (June 2016)

Once data has been entered in Samples worksheet, the entire XLS file can be uploaded to the appropriate Project (drag and drop uploading is enabled).

The validation process may take awhile depending on the size of file. We have not tested what the maximum size of files we can process but you can upload your data in batches if it makes management easier or, for example, your project is a yearly monitoring effort.

The uploading and validation process is detailed here in Documentation

Saving your data to project

The last step after the portal has validated your uploaded data, is for you to review the calculated summary stats and spatial bounds of your data. Save your data if it’s all correct. This will generate a digital object identifier (ARK) for you to reference in publications. Again Documentation outlines the details.

Send us feedback or let us know if you have any questions: amphibiaweb@berkeley.edu

Data Use Policy and information

Tue, 24 May 2016 08:43:59 +0000

Data Use Policy and Information

A necessary part of a project that solicits, stores and shares data is a clear understanding of the data sharing and use policy.

Goals

The aim of the Amphibian Disease portal is to facilitate data sharing of chytrid disease presence and absence from field and lab studies, which we view as the first step to effectively address the global amphibian crisis. We aim to encourage collaboration and facilitate coordination among researchers and agencies involved in amphibian disease studies, particularly chytridiomycosis.

Data

1) Contributors and Users
We refer to individuals who upload datasets and project information as Contributors. We refer to individuals who download or otherwise use data on the portal and the website as Users. We will never share Contributor information that is not public on the site.

2) Ownership of Data
The Amphibian Disease Portal (http://amphibiandisease.org) is developed and maintained by the AmphibiaWeb Project, Museum of Vertebrate Zoology, University of California, Berkeley. As a non-profit, educational and research entity, this is a public domain database and website that supplies data freely. We offer no guarantees or warranty, implied or explicit, about the completeness or accuracy of data nor its most appropriate use. We provide data for use in research and education only requesting attribution to the Contributor. We appreciate acknowledgement to the Amphibian Disease Portal and AmphibiaWeb.

3) Accuracy
To the best of their abilities, Contributors will provide accurate and complete data. The expectation is one of good faith representation of data that you fully own and control to be uploaded to the Amphibian Disease Portal. Geocoordinates for sensitive species or sites may not be purposely obscured. If there are legitimate reasons to protect localities, it is preferred to encumber data, i.e., keep private (see Embargo Policy).

4) Data Licensing
Contributors upon uploading data to the Portal agrees to these terms and specifically allowing us to assign unique digital object identifiers to projects and datasets under Creative Commons Attribution 3.0 (http://creativecommons.org/licenses/by/3.0/)

5) Public Availability and Embargo Policy
We recognize that data on some point records may be deemed premature for public use, such as graduate student dissertations or other active research projects. We need to balance that with the intent of the Portal to facilitate collaborations and aggregate data to study disease. Thus, basic information on Projects will be publicly viewable (e.g., Principal Investigator, Contact name, basic abstract, generalized area of interest to be determined by Contributor) and will be accessible on the portal without user registration and be subject to search engine results. Datasets (point records) associated with projects are private by default until the Contributor chooses to make those data public. Once made public, it may not be revoked. We recommend projects and their datasets be made fully public within 2 years or whenever the datasets are first published (including dissertations). If Contributors have not made their data public within 2 years and have not requested a continuance, we reserve the right to make these data public.

Send us feedback and any suggestions. Email Michelle Koo

Progress report on portal development

Mon, 18 Apr 2016 07:00:00 +0000

Spring update on the Amphibian Disease portal: We are in alpha release with core features working! The beta version is in progress now. Most importantly we have outlined the framework for the portal, which is sketched out in a user’s workflow diagram.

Here are the highlights:

Creation of Projects by Principal Investigators, where areas of effort can be identified and mapped
Uploading of Datasets, which are linked to Projects
Assigning of unique, resolvable identifiers to Projects and Datasets (e.g., minting doi’s)
Searchable map for Project sites in the Project Browser page
User registration and contact information
Project editing by PI

Projects Projects are the way we organize data and enable users to find past and future field and lab activities. They can be specific to a region and one-time sampling effort, e.g., “Andean frog chytrid testing in 2014”, or set-up as an ongoing monitoring project, e.g., “Monitoring for Bsal in the Golden Gate National Recreation Area” (neither of which are actual projects!). Basic information on PI and contact details as well as region and description of purpose are always publicly viewable but they may have all associated datasets declared private and thus masked from public maps or searches.

Projects allows PIs to assign other users to upload datasets if students or others are to collate field and lab results.

Projects also can be associated with publications or other DOI and thus serves as a means to deposit negative and positive results.

All Projects can be viewed, searched or mapped on the Project Browser

Private vs. Public data Whether datasets, that is the sampling record of species, location and disease status, are publicly viewable or private and masked from the general searches is determined by the Principal Investigator when creating the Project. This allows datasets to be encumbered and private while dissertations are written or publications are in review. Private datasets will likely have a default time span of 1 or 2 years after which time, if not renewed explicitly, will be made automatically public. Once made public, any data cannot be made private again (this is more a function of the nature of the internet and that Google bots do such a good job of scraping the web than anything we can control).

Project footprints The Project bounding box or area of effort can be defined in multiple ways during Project creation. These polygons will appear on the Project Browser page as orange areas for public projects and purple for private. Projects should not be created without a defined area of effort.

Users can define the Project areas by either: 1) searching on a Locality Name so that Google Map can automatically calculate its bounding box; 2) enter a list of coordinate pairs to define a bounding box; 3) use the Map interface to drop pins to define an area by clicking on the map then use the Build Map tool to create the footprint; 4) lastly, by uploading a dataset in an XLS spreadsheet where the minimum convex polygon will be automatically calculated.

Coming soon: More information on User registration and profiles, Data use policy, and Uploading data with our XLS template, and DOIs and Publications.

Send us feedback and any suggestions! Email Michelle Koo

The US takes action to ward off salamander disease crisis

Tue, 26 Jan 2016 08:43:59 +0000

In an unprecedented wildlife policy move, the US Fish and Wildlife Service (USFWS) has come out with an interim rule that lists 201 salamander species as “injurious” to wildlife due to the risk of a pathogen (the chytrid fungal pathogen that is lethal to salamanders, Bsal) under the Lacey Act. In the rule that takes effect on January 28, 2016, the import or interstate trade of listed species (live, dead, or parts) is prohibited, though permits may be granted for scientific, medical, educational, or zoological purposes. There is a 60 day public comment period, which ends on March 14, 2016. The rule can be found here.

Comments can be submitted online here.

Comments can be viewed here.

In addition to the USFWS ruling the US Geological Survey (USGS) came out with an open-file report in which they call for a proactive approach to prevent Bsal from entering the US and containing its spread if it is found in the US. They cite the need for cooperative research and management efforts to develop and implement effective prevention and containment strategies. In the report, the USGS identifies top research priorities and states that they are currently developing a Bsal Strategic Action plan, an emergency response plan, a monitoring and surveillance program, a standardized diagnostic approach, decision models for natural resource agencies, and a reporting database for salamander mortalities. The hope is to develop effective management strategies for Bsal which could influence or be adapted for other emerging infectious disease in wildlife.

This is an exciting time for biodiversity conservation, management, and policy!

The European Council Recommends Salamander Trade Restrictions to Minimize the Spread of Disease

Mon, 21 Dec 2015 08:43:59 +0000

The Bern Convention on the Conservation of European Wildlife and Natural Habitats is binding international legal text that was adopted over thirty years ago to protect Europe’s wild plants and animals. In December 2015 the Convention had its 35th annual Standing Committee meeting at the Palace of Europe in Strasbourg, France. With Bsal already decimating wild European fire salamander populations in the Netherlands and its spread to the UK and Germany via the pet trade, the Convention’s Standing Committee has officially recommended best management practices and restrictions on trade. The Committee stresses the importance of implementation and enforcement in order to conserve amphibian biodiversity.

The recommendations include immediate salamander trade restrictions until risk assessments and prevention/mitigation protocols are developed; pre-import screening for infectious diseases in live animal trade; establishing monitoring and surveillance programs both where Bsal has been introduced and in high risk areas that are still Bsal-free; applying biosafety rules to field work, breeding sites, and captive collections; and developing emergency action plans.

Says Tom Langton, a conservation ecologist and expert consultant on amphibian and reptile conservation priorities to the Bern Convention in 2015: “A huge debt of gratitude must be paid to the Council of Europe and the Swiss government for their prompt intervention. The massive risks to biodiversity from the increasingly damaging international pet trade are long known. Costs will be cripplingly high and with no guaranteed outcome. One has to look to the failure of CITES and EU controls over 20 years in arriving at such inevitable crisis. The meagre economic benefits of the often damaging trade in wild animals are not sustainable. Europe needs a similar system to Australia, where wildlife management is more professional and credible.”

Other countries have yet to take action against the spread of this lethal wildlife pathogen. Despite the impending threat of Bsal being introduced to North America, where almost 50% of the world’s salamander species occur, no action has been taken to avert this crisis. Hopefully other governing agencies will see the importance of preventive action and join in on the international effort to mitigate the spread of infectious diseases in wildlife and conserve biodiversity.

Recommendations No. 176 (2015) of the Standing Committee, adopted on 4 December 2015, on the prevention and control of the Batrachochytrium salamandrivorans chytrid fungus

Click here for the UK Animal Protection Agency’s press release.

US Pet Industry Calls for Immediate Ban on Newt Imports

Fri, 20 Nov 2015 08:43:59 +0000

The Pet Industry Joint Advisory Council (PIJAC) has recommended that all importers, exporters and buyers place a voluntary temporary moratorium on firebelly and paddletail newts (Cynops orientalis and Pachytriton labiatus*, respectively) to thwart the spread of Bsal to US salamander populations. They also ask all businesses to regularly sanitize their facilities as a precautionary measure while government agencies, industry, and researchers work towards effective Bsal testing and treatment protocols.

Click here for more information.

*AmphibiaWeb notes that Pachytriton labiatus is now being recognized as Pachytriton granulosus.

The US is working towards a ruling on salamander imports to address Bsal

Fri, 13 Nov 2015 08:43:59 +0000

The US is evaluating which salamander species to list as “injurious” under the Lacey Act. Since there are no current international or US laws or regulations in place to call on emergency protocols for emerging infectious diseases in wildlife, the US must rely on the Lacey Act to prevent Bsal from entering the US. Despite the calls to action by various amphibian and disease experts to place a temporary ban on live salamander imports into the US until we have a better understanding of Bsal disease dynamics, the US Fish and Wildlife Service has not yet taken any formal action.

Click here to check for any updates on the ruling.

Bsal Workshop Presentations Available

Fri, 13 Nov 2015 08:43:59 +0000

Amphibian experts from the Amphibian Survival Alliance, the Association of Fish and Wildlife Services, the PARC National Disease Task Team and their partners held a workshop in Asheville, NC in August of 2015 to bring experts and stakeholders together to address the threat of Bsal to North American salamander biodiversity.

Presentations covered the current state of scientific knowledge as well as national and international policy regarding biosecurity and wildlife trade.

Click here to view the slideshows.